On my Schecter Hellraiser Extreme (Floyd Rose) my second octave is very, very flat. I already adjusted the saddle forward all the way but it's still like this. I hadn't replaced my strings for a while, could that be it? It's unstrung right now and I was about to replace them but while its unstrung is there anything else I can do? Would adjusting the truss rod help? I don't wanna screw it up, and if so which way do I turn?. I hope it's neck is okay since its neck through and the guitar is worth like over $1000

Was it always flat? That's not really a problem that should just pop up randomly. It means, in layman's terms, that the bridge saddle is too far away from the nut. A truss rod adjustment, crappy old strings, or a mildly warped neck wouldn't likely cause the issue. Not sure how you would go about fixing it. How flat is it exactly? When does it start to sound flat on the fretboard?
First thing to try on any problem of this type is fresh strings, so just start with that.

If there's a neck relief issue (very unlikely to be the cause of the problem), the only way to find out is by actually measuring the relief.

Is the Floyd's baseplate properly parallel with the body?

Might seem obvious but are you definitely on the last intonation screw hole?

Which string is the problem?
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First thing to try on any problem of this type is fresh strings, so just start with that.

This was my first thought when I saw the thread title.

as strings get worn, the intonation starts to go flat. this is most likely the reason for the problem. especially if everything was ok before.
I like analogue Solid State amps that make no effort to be "tube-like", and I'm proud of it...

...A little too proud, to be honest.
I have an old as hell (ten years+) bass with the original strings made of muck and rust. It sounds like garbage, but the intonation didn't change. Grime and rust doesn't effect intonation. (Though they will sound terrible.)
Yeah alright guys I'm gonna just restring and see what happens :/

I'll be back if it doesn't work haha
Old strings. I have no idea how many times I've "fixed" intonation on guitars people brought me just by changing strings. Since I refuse to adjust intonation without new strings anyway, that's all I have to do 90% of the time, change strings.

Don't touch the truss rod unless it needs it. The truss rod has absolutely nothing to do with intonation, it's intended to adjust neck relief only. Has almost no affect on action either, what little it does have you won't be able to feel. Truss rod is one of the biggest myths and misconceptions about guitar. Its one and only purpose is to give the strings some room to vibrate in the middle, called neck relief. Don't believe anyone who tells you anything else.

Strings vibrate in a pattern similar to a jump rope. Almost none at the nut and bridge, wider in the middle. That means if the neck is perfectly straight, there is a greater chance the strings will buzz against the frets in the middle of the neck, about the 7th to 9th fret area. So the truss rod was developed to allow the neck to "bow" slightly away from the strings, to allow more vibration room. Very little is actually needed, .015" clearance at the 7th fret is usually enough. If you're using .010 gauge strings, that's smaller than your G string, barely more than the B string. If you don't have fret buzz, forget about the truss rod. If you do, it's possible, but also can be caused by several other things and in different locations.

It can be checked using a capo. Put the capo at the 1st fret, then fret the top or bottom string at the area where the neck joins body. You should have .010" to .015" around the 7th fret between bottom of string and top of fret. If your B string will fit in there without scraping, or very lightly scrapes, G string scrapes and you can see the string rise, you're good. Use the pieces you cut off the strings when installing. Or use feeler gauges. Some people can get away with less, some need more, depends on playing style and string height.

After replacing strings, you'll have to re adjust intonation since you moved the saddle, and make sure the bridge is adjusted right.
Hmmm...I wonder what this button does...
Alright guys yeah I replaced the strings and it's good now! I was also under the impression that dirt and rust wouldn't change the intonation but I was wrong. I worry too much haha