So i recently started battling for reel with one of my pets, and i got myself a Molten Summoning Tome, i battled Forj Matriarch, the Dormant 70 times then got a Molten Summoning Tome Stage II. I had to buy a lot of new water damaging Weapons. Now to my question.

I modified my Weapons with Water Baguette Crystal´s to do more damage, but if i remove the weapons from my Default Weapon Set, will they still be modified when i equip them to the pet again, or will they be back to basic?

If you remove them from your default weapon set they will still have their modifications. If you remove them to your inventory then they will lose them. :)

Awesome thank you so much for the answer. :) .