Not into electric guitars but a lot of them have intonation adjustment screws at the bridge. If sharp at the 12th fret,the saddle needs to move back.You are OK with checking the intonation the way you did,so if you are a bit handy try adjusting the saddle or saddles back a bit. When the guitar was worked on maybe the string heights etc were checked but not intonation. Maybe you ear is better then his. A good ear is both a blessing and a curse..............!!! Good luck with your work.
Tom
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