I just have a general question, for the record I play alot of guitar but I have no clue when it comes to actual guitar setup procedures.
Now, I've had really bad intonation problem on B and thin E string for some weeks and its a floyd rose bridge. Thin E string measures 0.009 in gauge and its new strings. Im actually not sure if thats the same gauge as when I bought the guitar. So B and E is terribly flat on 12th fret, about 1/4 tone flat and the saddle is moved as far towards the neck as it can go.
Nothing I have tried seems to work, I have already adjusted the bridge so its level and straightened the tross a bit and as said changed strings.
What can I do here? No video or article I have looked at covers something like this. If I move the saddle up away from the neck the intonation becomes perfect immidiately but 1 halfstep lower than its supposed to be.
Did you get a new set of strings or did you just replace the B and high E strings? Normally, bad intonation is a sign to replace the whole set.

Try re-adjusting the intonation but this time, after each adjustment, check if all the strings are perfectly in tune, not just the one you just adjusted. As with everything on a floyd, one change affects everything else.

If all else fails, I find that intonating on the 24th fret (if you have one) works just as well if not slightly better then intonating at the 12th fret.

Also, learn how to do a complete setup.Read this guide. I've found it quite helpful in the past.
Have you moved the saddles forward by removing the set screw and moving it to the one closer to the neck?
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The whole set of strings is changed. Tbh first I just changed B and E and then changed the rest a week later or smth.
As for the saddle yes i loosed the screw and put it in the hole closest to the neck.