(I had raised this issue in the past and have finally had time to come back to it and strip down the classes to a minimum).
The problem seems to lie in having bidirectional links (viz, I have @OneToMany Map<String, Entry> children and @ManyToOne Entry parent in my classes. I've attached the offending classes. If I add an entry to the children I get an error. I'm wondering if it's a question of multiple references to the same instance of a class? It's hard to tell with the opaque code of ObjectDB.
Exception in thread "main" [ObjectDB 2.3.6] javax.persistence.RollbackException Failed to commit transaction: Attempt to persist a reference to a non managed Folder instance - field Folder.children (error 613) at com.objectdb.jpa.EMImpl.commit(EMImpl.java:279) at F380.main(F380.java:20) Caused by: javax.persistence.PersistenceException: com.objectdb.o.UserException: Attempt to persist a reference to a non managed Folder instance - field Folder.children at com.objectdb.o._PersistenceException.b(_PersistenceException.java:47) at com.objectdb.o.JPE.g(JPE.java:140) at com.objectdb.o.JPE.g(JPE.java:78) ... 4 more Caused by: com.objectdb.o.UserException: Attempt to persist a reference to a non managed Folder instance - field Folder.children at com.objectdb.o.MSG.d(MSG.java:61) at com.objectdb.o.TYW.writeElement(TYW.java:257) at com.objectdb.o.MPT.writeStrictly(MPT.java:243) at com.objectdb.o.TYW.ar(TYW.java:393) at com.objectdb.o.TYW.av(TYW.java:474) at com.objectdb.o.TYW.writeElement(TYW.java:273) at com.objectdb.o.UMR$P.y(UMR.java:960) at com.objectdb.o.UMR.x(UMR.java:549) at com.objectdb.o.UML.u(UML.java:515) at com.objectdb.o.MMM.af(MMM.java:1033) at com.objectdb.o.UTY.aG(UTY.java:1195) at com.objectdb.o.UTY.aF(UTY.java:1184) at com.objectdb.o.ENH.a(ENH.java:46) at com.objectdb.o.STA.T(STA.java:512) at com.objectdb.o.STM.E(STM.java:425) at com.objectdb.o.OBM.bI(OBM.java:888) at com.objectdb.jdo.PMImpl.bI(PMImpl.java:2186) at com.objectdb.o.OBM.bH(OBM.java:804) at com.objectdb.o.OBM.bF(OBM.java:719) at com.objectdb.jpa.EMImpl.commit(EMImpl.java:276) ... 1 more