The notice for me to upgrade to Firefox 3.6 says specifically that the "extension Zotero 2.0b7.2" (mine, I guess) is incompatible with Firefox 3.6 and upgrading to Firefox 3.6 will cause the Zotero to be disabled. They're pushing the Firefox upgrade as important for security reasons. I see in messages "upgrade to Zotero 2Orc" something. Is that different from what I see on the Zotero website as the most recent version "2.0.2"? Is that any different from what I already have? What do I do? haven't accepted the Firefox 3.6 upgrade yet.
2.0.2. is the mos trecent version - RC was slightly earlier - apparently the message hasn't yet been updated - but the effect is the same.
b7.2 is a slightly outdated 2.0 - but changes to 2.0.2 are minimal so updating won't be a big deal. So first update to 2.0.2. then to FF 3.6 - I wouldn't expect any problems, though it's always a good idea to have a back-up of your data directory, so if you don't have one anyway you could take the opportunity to do that before the upgrade.
I installed Firefox 3.6 and Zotero disappeared from the task pane. But once I installed the latest version of Zotero, everything worked fine, and my library is completely intact.
In general I'd recommend the reverse, since the upgrade should be faster (and potentially more reliable) in 3.6. If you're using Zotero 1.0, it will temporarily disappear (and be listed as incompatible) once you install 3.6, but it will reappear as soon as you upgrade to Zotero 2.0.
Upgrade Storage
also, Zotero 1.0.10 doesn't work with FF 3.6 - upgrade to 2.0.2 if you're still using the old Zotero.
b7.2 is a slightly outdated 2.0 - but changes to 2.0.2 are minimal so updating won't be a big deal. So first update to 2.0.2. then to FF 3.6 - I wouldn't expect any problems, though it's always a good idea to have a back-up of your data directory, so if you don't have one anyway you could take the opportunity to do that before the upgrade.