Nut can usually accommodate a little change, as brands may also differ in thickness...
So if you have gone from a std 45-65-85-105 Rounds to say a 45-65-80-100 Flats...
Check for a twisted string, do you wind a wind round the peg by hand, this can introduce a twist... slacken off a string, pull down to the bridge and see if you can un-turn half a turn at the ball end...
Witness points, tune- up and a light press - lighter with flats - at the bridge and nut contact points.
Saddles, got any silk over the saddle?
If the above don't fix it, trip back with a razor blade, although this may expose a rough join...