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What is a "Metablade?" Some kind of third-party class? Wrong forum, if so.
The answer to your question, assuming that Metablade literally says "feature X replaces Magus Arcana": No, you can't use the "1/6th of of an Arcana" favored class bonus to get an arcana because you don't have the class feature in the first place.
When do I count as having a class feature?
You have a class feature when your class description tells you you gain that class feature, generally based on your level in that class (and perhaps altered by factors, see below).
If you have an archetype or other rules element that replaces that class feature, you do not have that class feature. For example, if your archetype replaces a rogue's sneak attack, you no longer have the sneak attack class feature (whether a requirement is as general as "sneak attack" or as specific as "sneak attack +1d6," you do not qualify for it). . .

Azothath |
Metablade arch by d20pfsrd so 3rd party content.
This ability replaces the magus arcana gained at 3rd, 6th, 9th, 12th, 15th, and 18th levels. so no Magus Arcana for you.
Belafon has the CRB FAQ on this. The APG has a lot of archetype FAQs.

Pizza Lord |
Hmm, if it was directly addressed I can see that ruling. But from the wording, it looks like you would gain it. Granted, it depends on the wording. If a racial bonus said, '+1 to your sneak attack damage' and you didn't have the sneak attack ability, taking it wouldn't grant you one, but it would be there if you did get sneak attack.
Similarly if a racial bonus said you got to add one spell to your list of spells known... it would be pointless if you didn't have spell casting (or a spells known list). Or if the racial bonus said your arcana counted as 1/4th higher level or something.
But if it said you gained 1/4 of a spell from the sor/wiz list as a SLA ability per day, then it would, whether your class granted spellcasting or spells per day day or SLAs.
The metablade doesn't say it prevents the character from having magus arcana, only that it replaces those gained at 3rd, 6th, etc. If there was one gained at any other level, it would still be there. And it doesn't appear that having a magus arcana ability is a requisite to gaining a magus arcana ability. Now, if you didn't have arcana pool or something, then obviously certain arcana would be useless, since having one wouldn't grant that.
But I am only going by a quick reading on my phone based on what's been quoted and posted.

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Hmm, if it was directly addressed I can see that ruling. But from the wording, it looks like you would gain it. Granted, it depends on the wording. If a racial bonus said, '+1 to your sneak attack damage' and you didn't have the sneak attack ability, taking it wouldn't grant you one, but it would be there if you did get sneak attack.
Similarly if a racial bonus said you got to add one spell to your list of spells known... it would be pointless if you didn't have spell casting (or a spells known list). Or if the racial bonus said your arcana counted as 1/4th higher level or something.
But if it said you gained 1/4 of a spell from the sor/wiz list as a SLA ability per day, then it would, whether your class granted spellcasting or spells per day day or SLAs.
The metablade doesn't say it prevents the character from having magus arcana, only that it replaces those gained at 3rd, 6th, etc. If there was one gained at any other level, it would still be there. And it doesn't appear that having a magus arcana ability is a requisite to gaining a magus arcana ability. Now, if you didn't have arcana pool or something, then obviously certain arcana would be useless, since having one wouldn't grant that.
But I am only going by a quick reading on my phone based on what's been quoted and posted.
As the Metablade never gets a Magus arcana, it never gets the ability to add to them. You don't have the feature until you get it from your class or archetype.
PDT - When do I count as having a class feature?
If you have an archetype or other rules element that replaces part of a scaling class feature, or delays when you get that class feature, you do not have that class feature until you actually gain that class feature.
Example: If you have a fighter archetype that replaces weapon training 1 (but not weapon training 2, 3, and 4), you don't gain the weapon training 2 ability until fighter level 9, which means you don't have the weapon training class ability at all until you reach fighter level 9. Anything with "weapon training" or "weapon training class feature" as a prerequisite is unavailable to you until level 9.
Example: If you have a cleric archetype that replaces channel energy at level 1 (but not later increments of channel energy), you don't gain the channel energy ability until cleric level 3, which means you don't have the channel energy class feature until you reach cleric level 3. Anything with "channel energy" or "channel energy class feature" as a prerequisite is unavailable to you until level 3.
Example: If you have a witch archetype that replaces your hex at level 1 (but not later hexes, major hexes, or grand hexes), you don't gain your first hex ability until witch level 2, which means you don't have the hex class feature until you reach witch level 2. Anything with "hex" or "hex class feature" as a prerequisite is unavailable to you until level 2.
The Metablade has no starting Arcana, so he can't take the preferred class bonus at levels 1-2.
Does it get it at level 3? No, it has been replaced; he can't take it at levels 3-5.Same thing for levels 6, 9, 12, 15, and 18. He never gets the Arcana feature, so he can't take the Preferred class bonus that adds to the,
BTW: a Blackblade has the same problem for levels 3-5 and all Magus for levels 1-2.
Similarly, you can't get an extra arcana through the feat until you get your first arcana from the class.

Mysterious Stranger |

This ability replaces the magus arcana gained at 3rd, 6th, 9th, 12th, 15th, and 18th levels.
After reading the archetype I have changed my mind about if this would work. The Ability states it replaces the magus arcana gained at specific levels, not that it replaces the entire class feature. The fact that it specifies it replaces the magus arcana gained at specific levels indicates it is not removing the base class feature. If it had stated it replaces all magus arcana instead of listing each one individually that would have indicated it is replacing the parent class feature and the favored class bonus would not work. So, RAW this looks like it should work.
This is also a third party archetype and those are notorious for being poorly written. That being the case there would have never been an official answer even if Piazo was still supporting 1st edition. With that in mind you are going to want to check with your GM about it. I could easily see a GM deciding that it does not work.

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That is a . . . poorly formatted archetype. Is it called a Metablade or an Arcane Warden? Does anyone have the actual document?
It takes away every Magus Arcana that would be gained but doesn’t actually say “this replaces Magus Arcana.” Which it really should. Diego and I have posted the FAQs. You can’t get Arcanas with the FCB. Or the Extra Arcana feat. But people can (and will) split hairs about the language to argue otherwise.
Edit: There’s quite a bit that doesn’t make sense. The archetype can only use Metamagic Strike while spellstriking. With touch range spells. With a melee weapon. So why is the very first metamagic listed Enlarge Spell? That literally does nothing. Ditto for Reach Spell. Focused Spell? Can’t spellstrike to affect more than one creature.

Mysterious Stranger |

This is the reason I do not allow 3rd party material in campaigns I run. RAW there is a valid argument that the parent class feature is not actually replaced. If the character had multiple archetypes that ended up trading away all normal arcana individually, I could see allowing an elf to use his favored class bonus to gain extra arcana. I am not sure if there are any combinations of 1st party archetypes that could cause that to happen, so it might be a moot point.

Pizza Lord |
Agreed, though I might certainly allow 3rd-party stuff, it would have to be directly and specifically looked over by me (Quality products, like 101 Cursed Magic items or 101 Spells for the Common Man, or other finely edited projects by some of our very own forum posters. No, I don't make commission.), but even then it's probably specific items or spells or abilities, not necessary all of them. Even then, I can always tweak or make my ruling, which I can do for even CRB material, obviously in my own game, which is likely what your GM will have to do here.
As 3rd-party material, it is hard to make a determination on whether it was considered or intended (at least I am going by what's quoted, and I did go to the Metablade link Azothath provided). While I don't blame the designer or anything, mistakes happen. An editor should have thoroughly read Magus class and favored racial bonuses and probably put a blurb in there about it being a method for a metablade to gain a magus arcana. Possibly they did and just assumed people would understand that it worked (or didn't). Or maybe it's mentioned in another section or intro and I can't really comment on that.
I don't personally have a problem with it working. One specific race using six of their level bonuses to gain one arcana every six levels at the cost of hit points (or skill points). That's three arcana over a 20-level career. That seems a fair investment, again as my personal call on it.