PokerTracker

I converted an PT3 database with over 1,000,000 hands in it,
however note tracker seems to ignore those hands and has only created notes on the 'freshly imported' hands.
Is there anyway of making it create notes for those historical hands?
Also if you change the purge automatic notes older the 60 days to any number other than 60, it always reverts
back to 60, it never remembers your last selected value. (I realize this is quite minor)

There is a setting to define a cutoff date for note creation - try setting that earlier to have it generate notes on older hands. If you have a large number of hands you may find it better to only have notes on more recent hands, though, since people's play tends to change over time.

The 'purge older than' setting should be remembered - I just checked an my setting is not 60 so it must have remembered it from last time I used it. I think that it is only saved when you actually run the purge, though.

For some reason which I'm not sure about, after PT4 spent the best part of a day converting my PT3
database. None of the hands seem to be in the new database. I don't know why.
I will re-import the hands. But this seems to be my problem

Are you certain there's only one PT4 database? If you have two PT4 databases it is possible that your PT3 hands were converted into the other one.