After a firmware update it is normal for all presets to be rebuilt. It is also normal for any newly loaded presets that were created in older firmware to be rebuilt on the first startup after they were imported. What you described is normal except, of course, for missing cabs. That is highly unusual - virtually impossible in fact. What it possible is that you use IRs rather than stock cabs, and it is quite possible that those are missing, depending on what steps you actually took after the update. For instance, if you performed a factory reset after updating, as recommended, your previously installed IRs were deleted. If you did not restore them from the backup file then, yes, they are missing.
My advice is to perform a factory reset again and then restore almost all items from the system backup file that was created during the update. In particular, restore the IRs. The items you don’t want to restore are the latest factory presets (setlists #1, 2, and 8).