Declarations not found in large files, PhpStorm 2018.3.3

So I have an old project with some pretty large files (5000+ lines). I have upgraded to the latest PhpStorm and it has not fixed my issue.

My issue is that method calls are not linked to their declaration and are highlighted as such. If I try to control+click on the method name it tells me "cannot find declaration to go to".

The correct USE line is at the top of the file and I know it should be working because if I simply delete the bottom 1/4 of the file it starts working. I have tried narrowing down what code causes it to happen in the file, but it really just comes down to how much code is removed, not which code is removed.

I have increased my memory via my options file to no avail, and I am running the 64 bit version:

-Xms1024m
-Xmx2048m
-XX:ReservedCodeCacheSize=1024m
-XX:+UseConcMarkSweepGC
-XX:SoftRefLRUPolicyMSPerMB=50
-ea
-Dsun.io.useCanonCaches=false
-Djava.net.preferIPv4Stack=true
-XX:+HeapDumpOnOutOfMemoryError
-XX:-OmitStackTraceInFastThrow
-Dhidpi=true
-Dawt.useSystemAAFontSettings=lcd
-Dawt.java2d.opengl=true

What can I do to increase the number of lines this software can deal with. Disabling inspections has no effect. Invalidating caches and restarting has no effect. Deleting my .idea folder has no effect.