Can you make sure you are running the most recent version of Zotero (2.0rc2) and then make sure you are in the correct Firefox profile. See the trouble shooting Zotero data issues section of http://www.zotero.org/support/zotero_data for more details on this. Please report back.
If you were shifted to a new profile you would still have a Zotero folder, that is created automatically. Try to see if you have other Firefox profiles, you can use this doc to run the Firefox profile manager to see if it was moved. http://support.mozilla.com/en-US/kb/Profiles
Otherwise, see if you have multiple zotero.sqlite files. You can always revert to one of the automatic backups Zotero generates. The backups will be called zotero.sqlite.bak or zotero.sqlite.SomeNumber.bak. Check on the size of these files, if you have a small zotero.sqlite file and a large zotero.sqlite.bak file you can swap them out. Make sure Firefox is closed and rename the zotero.sqlite to some other file name and change the larger zotero.sqlite.bak file to zotero.sqlite
Upgrade Storage
Otherwise, see if you have multiple zotero.sqlite files. You can always revert to one of the automatic backups Zotero generates. The backups will be called zotero.sqlite.bak or zotero.sqlite.SomeNumber.bak. Check on the size of these files, if you have a small zotero.sqlite file and a large zotero.sqlite.bak file you can swap them out. Make sure Firefox is closed and rename the zotero.sqlite to some other file name and change the larger zotero.sqlite.bak file to zotero.sqlite
Back up all your directories and upgrade to Zoter 2.0rc