Don't worry they can transfer over your points if you provide your old and new Steam IDs.


When I moved from non-Steam to Steam, I kept my old non-Steam installation. But that's just because when a Steam update would come out, I'd be able to admin the server that wasn't updated yet, whilst all the other admins were on the updated servers.

I'd probably just delete it, unless it took you a long time to download it, in which case just keep it.