Found all mine in e:/sys/bin
You can't use them (easily), but they are still there. If you reinstall, the configs appear to be kept. I reinstalled eZSpot, and everything was still configured. Same with angry birds (all my levels were saved). Can't guarantee it - if you have a backup you should have the files. Connect to a PC, and look around. Search for a file containing one of your links (ie. bookmark file), then copy it. If you lose them when you reinstall, then you have a copy.
Alternatively, if you know what you are doing, create a sis file with the missing app from e:/sys/bin and reinstall. Deleting the app might prove troublesome later (ie. all the files associated with the app weren't deleted), but you will have your app back.
PS. Try this at your own risk - I did, and it worked for me, however there are no guarantees
Personally, I'd wait - Nokia are apparently looking into this (many complaints on the nokia support boards). Might be a fix later.