As we've progressed through Curse of the Crimson Throne, we've seen the number of weapons diminish. We've removed weapons as instructed as we hit each new quest. Our group has been pretty successful at finding upgrades, so almost all the 1-3 weapons are removed from the game. We have Hakon, Selah, and Harsk all carrying 5 weapons, while our other three characters each have 2.
Tonight, setting up 6B, we finally ran out. Using the middle card row, almost every location required a weapon, and I think the cliffs needed two, and the arsenal three. There just weren't enough in the vault. We ended up putting one weapon in each location, then making up for the shortfall with blessings (after making sure we'd have enough for the hourglass if we did this). But, is there an official ruling?
By my count, there are 21 level 4-6 weapons in the Curse of the Crimson Throne box - remember that Loot cards are shuffled into the vault with other cards of their level now (however, you consistently earn then 'before' they would normally get shuffled in).
So if 4 players had 11 weapons (and lets assume 0 of which were from lower levels), that means there should be 10 remaining in the vault.
For 6B, the locations in that scenario, for a 4 player game using Medium locations (Library/Mountain.Cliff/Cell/Castle/Arsenal) require 0+1+1+1+1+3 == 7 weapons.
In other words, in the situation you presented, there should be more than enough weapons in the vault to create that scenario, and then have at least 4 weapons leftover. Because of this, I would check to make sure...
Now, in the hypothetical scenario that you run out of cards, the closest thing to an official ruling (such as if you were playing Organized Play) is that you simply do not add cards that do not exist, as per the Limited Resources rule. So some locations would have less cards in them.
A more sensible implementation in home games would be to add some lower level weapons or use another card type, as you did. However, I'd double-check your list of 4-6 weapons compared to the Curse of the Crimson Throne cardlist, because my count shows that you should have had enough weapons, with some to spare.
Officially, the rule is found on page 14 in the Counting Resources sidebar: “If you’re required to do something with a certain number of things and there aren’t that many things available, use as many as there are.”
In other words, if you run out of Weapons to build locations with, you don’t replace it with anything—those locations simply will have fewer cards in them.
Unofficially, I would just grab some of the level 3 weapons I removed from the game and re-include then in the vault before building the locations. With 6 characters and no class decks being mixed in, this is probably your best option.
Otherwise if you have a class deck (I’d suggest Ultimate Combat or Ultimate Equipment) and don’t mind doing some mental work with the transition guide and FAQ, mix those cards into the vault according to the usual vault building rules.
That is an unusually high number of weapons for one party. It is perhaps worth note that removal of low level boons is entirely optional ; if you're that low, I'd encourage you to pick your favorite lower level weapons and toss them back into the box, or to take one of the other offered options.
By my count, there are 21 level 4-6 weapons in the Curse of the Crimson Throne box - remember that Loot cards are shuffled into the vault with other cards of their level now (however, you consistently earn then 'before' they would normally get shuffled in).
So if 4 players had 11 weapons (and lets assume 0 of which were from lower levels), that means there should be 10 remaining in the vault.
For 6B, the locations in that scenario, for a 4 player game using Medium locations (Library/Mountain.Cliff/Cell/Castle/Arsenal) require 0+1+1+1+1+3 == 7 weapons.
Six character party, with the ones I named carrying 15 weapons, the other three having 6 between them (Varian, Kyra, and Sajan, who has the Blackjack weapons), so it's 21 cards in character decks. And six characters adds the Repository, needing another 2 weapons, and I don't recall the last location. Weapons have been a priority, so we've worked at upgrading those, wiping out most of the lower cards as we advance (except I think Kyra still has deck 1 weapons).
The other solution we came across was building for small locations, as we found the rules for this one particularly annoying (exacerbated by some truly atrocious die rolling)
Six character party, with the ones I named carrying 15 weapons, the other three having 6 between them (Varian, Kyra, and Sajan, who has the Blackjack weapons), [...]
Ah, yeah; I'd like to apologize for misreading your initial post. Despite re-reading it multiple times I somehow thought you were playing with a Harsk with 5 weapons + 3 other characters, and I skipped over the mention of Hakon and Seelah.