So my les paul has a tune-o-matic bridge.. and probably from the first string change... I must of accidently put the saddles back on the wrong way round. Does this affect tuning stability or intonation? I can't swap it back either as the strings have already made notches in the saddles which fits each strings' individual size.
As long as the saddles are in the same position both ways, no. They will face the same way even when flipped around.
if you're that concerned just detune, whip it of, switch it round then tune up again.
There's no "backwards" with a TOM bridge. As long as it intonates it's fine.