Hi there!
If this problem is still present for you (who reading this topic) - I wanna to point on my solution.
I have same symptoms: a big project (1 skeleton, 3 characters inside it, lot of a layout things (background, properties e.t.c.), tons of TC, IK e.t.c.) and yes - once upon a time my project begins to fail savings. Log file says:
ERROR: Error saving project:
java.lang.OutOfMemoryError: Java heap space
at java.base/java.util.IdentityHashMap.resize(Unknown Source)
at java.base/java.util.IdentityHashMap.put(Unknown Source)
at agh.C(SourceFile:19)
at afY.C(SourceFile:453)
at afY.I(SourceFile:427)
at agl.C(SourceFile:22)
at agl.C(SourceFile:11)
at afY.C(SourceFile:397)
at aha.C(SourceFile:430)
at agR.C(SourceFile:173)
at afY.I(SourceFile:428)
at agl.C(SourceFile:22)
at agl.C(SourceFile:11)
at afY.C(SourceFile:397)
at aha.C(SourceFile:430)
at agR.C(SourceFile:173)
at afY.I(SourceFile:428)
at agl.C(SourceFile:22)
at agl.C(SourceFile:11)
at afY.C(SourceFile:397)
at aha.C(SourceFile:430)
at agR.C(SourceFile:173)
at afY.I(SourceFile:428)
at agl.C(SourceFile:22)
at agl.C(SourceFile:11)
at afY.C(SourceFile:397)
at aha.C(SourceFile:430)
at agR.C(SourceFile:173)
at afY.I(SourceFile:428)
at agl.C(SourceFile:22)
at agl.C(SourceFile:11)
at afY.C(SourceFile:397)
or just says:
ERROR: Error saving project:
java.lang.OutOfMemoryError: Java heap space
Then, sometimes it saves with no problem.
So, after hour of researches AND Nate's point of view /* that if the problem with saving of project - smart (!) Spine don't want to save because of non-good state of something in the project*/, I've found problem!
The problem is: I have tons of animations inside the project: over 100 (versioning of worlkflow). And on some step I deleted some slots, that was used in beginning steps of my project, but not used in the next steps (so I deleted this slots). But the animation with this deleted slots was still presented on my animations branch of tree. And, as I decided, when saving the project - Spine had do something with this old version animations and get the error with this DELETED slots. All I done - I deleted all previous animations (as I don't remember in what version of animations I used this deleted slots - I've deleted all before last=current animation) and leave only current version of animation. So - my project have no problem with saving, also it began to save RAPIDLY (before deleting of all previous animations it was SLOOOW).
Thanks Esoterics for Spine - it awesome!