|Tomppa Venture-Lieutenant, Finland—Turku|
Apparently, large weapons aren't uncommon - you can just buy more large weapons.
Finding magical weapons during adventures (aside from the basic +1 or striking) is pretty rare anyway, but if you do happen to find one, you can choose either using it (and losing the benefit for having a large weapon) or continuing to use your large weapon instead. However, since you don't get to keep the stuff you find during an adventure but rather must buy the stuff after the scenario, you can just buy large magical weapons when you have reached high enough level and have enough gold.
Since basic +1 and striking weapons depend on runes, not the magical weapon itself, you could just buy the runes at lvl 1 and 4 and slap them on your large weapon.
Rules for items of different sizes states that if a magical item is significantly more than 8 times the price of a mundane version, you get to use the same price without adjustment for a larger version.
Similarly, if you do happen to find a specific magic weapon (which are pretty rare sight in chronicle sheets) it'll almost certainly cost significantly more than the "8 times the price of the mundane version" so you can purchase a large version after the adventure if you want to.
It's just that rarely you may come across a cool weapon during an adventure and not be able to benefit from the large bonus if you decided to use it. Then again, similarly a fighter may come across a cool weapon that isn't part of their chosen weapon group, and will have to choose between expert + cool weapon or master + their own weapon. Or a rogue/Swashbuckler may come across a cool weapon that isn't agile nor finesse and have to choose between sneak attack/Precise strike or using a cool weapon with cool extra powers. Or a regular barbarian may come across a cool weapon that's agile and have to choose between cool weapon + worse rage, or their old weapon + better rage.