Go ahead and redownload it. If you've already made changes to the tables for bases and stuff, the only thing that was updated was Autolevelling and Saves/Autolevel and Save EA.txt, so you can just copy that file over.
What happened was that it was believed that byte 0x39 in character RAM data wasn't used, so Brendor and I used it for our splits. It turns out it is, in fact, used; it's a bitfield whose bits correspond to each support partner, and is set if you get a support with that partner during a chapter so that you can't get two supports with the same person in the same chapter.
Rather than rewriting the split to use another (theoretically) unused byte, which would have been long and painful, I opted to move the offending bitfield instead. It uses byte 0x1C, which is also theoretically unused. I haven't rigorously tested it, so let me know if there's more issues.
If you find an issue (ie, it seems byte 0x1C is used for something) and are feeling brave, you can open Autolevelling and Saves/Autolevel and Save EA.txt, go to line 30, and change 0x1C to either 0x3A or 0x3B (both are also of unknown use) and see if that fixes the problem. Be sure to let me know, so I can update the main file and my notes.