This is a hard problem and something that I think has to be intrinsic to the serialization method of your CRDT. Unique IDs of any kind are really risky in CRDTs because they basically break the mathematical links between potential partitioned duplicates. Lists make this problem even harder because you have to contend with if you should incorporate the ordinal of each element into the hash value.
I’m working on a version control system for visual programs. You wrote a response to someone on structured edits a few months back about how the UNIX fs not being schema/structure aware is the core problem with collaborative edits and destroys open interoperability. I think you hit the nail on the head. I’ve been working on something for nearly a year now to try to address that problem. Let me know if you want to compare notes.