I had a similar bug more than 10 years ago, also while building a search index through Lucene. It would crash after hours of running with an impossible nullpointer exception. It always appeared after running for hours, and running that specific iteration would not trigger the exception, so hard to reproduce.
Turned out it was a java jvm bug which was triggered when the jvm decided to recompile that code part since it was used more frequently.
Try running your code with the -server flag and see if that makes a difference.
Reminds me of a time where I almost certainly found a bug in Safari Mobile's JS implementation. Some variable ended up undefined in a place where it was provably impossible. It didn't happen consistently and was prone to right timing, so extremely hard to pin down and debug. Given the fact that all debugging had to be done tediously through a phone emulator and remote dev tools (it was inside a Cordova app), I eventually just gave up and added some sort of if-else for that case.
-server is only a thing for HotSpot. They mention that HotSpot works perfectly fine. There is no option of "-server" for Graal native-image. It has "-O{0,1}" though for turning optimizations off and on respectively.
I think the project does have a bit of a naming problem. They've gotten the part out where it's very fast and pretty good, but everything is named GraalVM-something and it's not always entirely clear what's being referred to.
Turned out it was a java jvm bug which was triggered when the jvm decided to recompile that code part since it was used more frequently.
Try running your code with the -server flag and see if that makes a difference.