-
I was going to ask if you changed string gauge. That can make a big difference. Heavier strings require more tension, and that will bend the neck more unless the truss rod is adjusted to balance the additional tension. That will make the strings seem like they have higher action (but that’s a misnomer – truss rods adjust neck relief, not action). When the strings are too far above the frets, it has an adverse effect on intonation of fretted strings.
I don’t think a change in string gauge should effect the other aspects of setup (saddle and nut height). If you go to heavier strings than what were on the guitar, it is possible some of them don’t fully seat in the nut slot. This would make those strings sit further from the frets, again possibly causing intonation problems.
I recommend the site frets.com to learn about various aspects of guitar setup. The information is well-organized, clear and authoritative.