I'm currently playing on a D'Angelico EX-DC. It has a Gibson-style bridge.

I changed strings about 2 weeks ago and set up my intonation then, checking it everyday for about a week after that. But eventually the saddles for my G, B, and high E strings had to be moved as far away from the fretboard as they can go. They still fret sharp at the 12th fret and I don't know what to do.

I've wondered if changing strings and readjusting the saddles for those strings as close as possible to the fretboard would somehow make a difference, but I haven't tried it yet. Looking for some advice on what I should do. I play a lot of jazz and I know I have to be pissing off some horn players in a combo I'm in when I play higher voicings with extensions. Any advice would be helpful. Thanks!
is the bridge flipped so you get the most throw out of the saddle?
2002 PRS CE22
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What gauge were the previous strings? Do you notice a change in action?
I wonder if the truss rod needs a bit of adjustment. It would be odd for it to throw it off by that much, but it's worth a look.
Is it possible that you flipped the bridge by accident when changing strings? Some TOM bridges adjust farther in one direction than another. Flipping the bridge might get you a tad more room for adjustment.
You don't keep checking it once it's set till you change the strings again. Did you intonate by using open string and fretted 12th? What did you check with; your ears, a chromatic tuner or strobe type tuner?
If you adjust using older strings you won't get accuracy which may explain why you ended up moving the saddles after playing for some time. If your action rose since intonating the fretted note would be more sharp as the deflection would increased but......
Moving on.....
If you have a Gibson ToM style bridge you may be able to reverse the saddles for specific strings if you need more room to adjust. I am not familiar with your guitar/bridge. This works for Gibsons when needed.
I tuned using a KORG TM-50. I need to get a strobe tuner, but that's a different issue. I'm using the same strings as before (D'Addario XL Nickel Round Wound Med Tom/Heavy Bottom), although the intonation wasn't perfect the last time either. This set of strings is just significantly more out of tune than the last set. I'm pretty sure I didn't flip the bridge, but I could try that and see what happens.