I haven't had any problems syncing my T3 with Fedora Core 2. The following assumes you have all the relevant software installed. Try the steps below, and reply with the results.
geeknik, you'll need to add the Pilot back into the list by:
1) Starting "Pilot Settings" (gpilotd-control-applet)
2) Click on Add
3) Click on Get from Pilot and fill in the boxes.
Secondly, check that the pilot conduits haven't been reset - mine were during the upgrade from RH9 to FC2:
1) Start Pilot Settings
2) click on the Conduits tab
3) check your synchronisation setup.
Thirdly, add the Pilot Applet to your Panel to allow Hotsync at any time:
1) Right-click on panel
-> add to panel,
-> Pilot Applet.