PokerTracker

I'm going to do this but quite concerned about all the notes that I've manually wrote in my database, will they disappear?

Also not sure if it you can answer this, but if I later prefer PT4 whenever it's released, can I than export from HM2 back to PT4 with all the notes intact?

Notes are specific to the database, and aren't exported as part of the hand histories. You can export them from a database as part of a Backup, but HM use a different database format so you won't be able to import your notes.
PT3 doesn't delete any hand histories, so you will still have the original files (in the PokerTracker 3\Processed folder by default) unless you deleted them yourself, and they are the best thing to import from. The same applies to HM if you later want to import to PokerTracker again.