This is actually a conflict with Essentials included big bag mod.
The Synergies big bag and Essential big bag r using different type of file structure, they can work at the same time rather than override. Therefore, Synergies big bag is not visible since there is no extra pages button for it while Essentials is above Synergies. So while ur bag appears to be full, the more items u pick will drop to the big bag of Synergies, which is invisible.
The Simplest solution to this is
1. Put all ur items from ur character, ur stash to share stash. Make a back up to ur sharestash, and load ur character with no essentials mod.
2. U can see those item u lost is in ur current bag now, pick them up and put them in ur stash or sell them, whatever. U will lose those essentials item in this 'invisible bag' anyway, but synergies or LAO items will be left.
3. After that, try to fill ur character's bag with trash items (Gem Sword, Reju potions, Waypoint scrolls or any cheap scrolls), make sure it's filled and u cannot pick up anything.
4. Exit ur character when all done and reload it with Essentials active and ur backup sharestash in previous steps. Enjoy ur 'newly made' bag now!