In the current versions of the game, the weapons created by the shapeshift spells will wear off in about 16 hours leaving you wielding your standard weapons while shapeshifted. To fix this issue in my own game I edited these files to give the weapons a permanent duration.
IMPORTANT NOTE: These files are intended for BG2:EE only! Installing them on BG1:EE will cause issues!!!
To install simply extract all the files into your BG2:EE override folder.
Please let me know if you have any problems with this mod so that I can fix them for you.
Quick note: my attempt to make the weapons undispellable did not work so I have removed that part of the mod. They should still have a permanent duration however.