PokerTracker

I have about 1.5 million hands saved for FTP but can no longer play there. I'll be starting fresh playing on the merge network. I'd like to keep all the stats on myself for study from FTP, but if starting a new database for Merge will improve performance I'd rather start a separate one.

Would I see much/any improvement if I start from scratch, or does it matter?

You could start a new database and still keep the existing database to refer to, although you wouldn't be able to see your overall stats together that way.
I wouldn't expect performance problems if you continue to import to the same database, though, as long as you keep the cache at 100% (status bar of PT3).
If you find that things are too slow for you you could start a new database later, and transfer your Merge hands to that.