Figured it out:
Use that tool to unpack the single saved game file in Documents\Larian Games.... Then use the same tool but the other tab to convert the global.lsf file that was unpacked to global.lsx. Then use a text editor to open the global.lsx file. In there, ctrl + f for "pocket" and delete the lines. I left one line (read: one pick pocket block) for each big pick pocket section (which I assume was for each character that has pick pocketed before) just because I didn't know what completely deleting that data would do. Finally, convert the lsx back to lsf and repack the files.
As a bonus, ctrl + f for id="IsPlayer" value="True" to find each of your characters and modify them if you want.
Last edited by hamburglin; 09/07/16 12:13 AM.