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Consider separating Jenkins master from any executors actually running builds. If you don't have the machines, run a separate Jenkins slave process on the master so they run in different VMs. I expect this to make investigating issues easier.
Regarding the heap, remember that build records are soft references, so it could go from a situation where two threads trigger GC of each others' data to peaceful coexistence. Or not. Still, worth a try.
FWIW if you don't need fingerprints, don't use them. (You can move the fingerprints folder out of Jenkins home and restart Jenkins to try – note that you'll lose either these old or any newer fingerprints as they don't merge easily)