the steps you list to re-flash the N900 without losing your data are the correct ones, indeed
(... -F ... -f -R )

you can indeed recover apps included in a backup simply by restoring it
(start BACKUP, click on the backup (directory name, in fact) and click on RESTORE.

UNCHECK EVERYTHING except applications, as you will otherwise reset you conversations, settings & all to the state prior of the backup, which is definitely NOT what we want.
maybe a good idea to make a FRESH backup of the DATAs (settings, convos aso.) prior to restore, just in case...

after the restore completes it will restart the N900 & a pop-up will appear, offering to restore the applications as well.