Here's the setup:
We use guild officer notes to keep track of to whom each of our alt's belongs. This works fine, except that we have a separate guild rank for all of our alts, and this separate rank does not have access to see officer notes.
The problem comes when we upload our character/guild data. As an example, if I am playing my main, GuildProfiler picks up the officer notes, then when my data is automatically uploaded when I log out, everything works fine. However, when I play one of my alts, GuildProfiler can not see the officer notes. When I log out now and upload my data, all the alt information gets wipes out of the roster.
The solution is probably to modify the member list module so that if the match field is officer notes, and the CharacterProfiler.lua file has the ["HasOfficerNote"] = false line in the ScanInfo section, that alt data should not be updated. I'll take a look and see if I can hack something together, but I just wanted to post this here in case there's a fix I'm overlooking.
Another alternative is to just have an option so if a bunch of characters get uploaded in the same CharacterProfiler.lua file, then they're all considered to be alts of one of the characters. That way we wouldn't have to mess with parsing notes at all. I had this working in roster 1.7.3, and could probably adapt the source code for the new version if anyone else is interested.