Re: Multiple vertices generated for the same index value and vertex properties missing with RF3
The workaround you found has implications for performance. So, if you can describe how to reproduce the issue, you can make an issue for it on https://github.com/JanusGraph/janusgraph/issues
This might easily be a scenario that is not covered by the current janusgraph tests.
I see that "id" is indeed a property key in the schema. I assume your input data already had this "id" property and this was not generated by janusgraph. In the former case does replacing "id" by "user_id" make any difference (this will make your queries more readable anyway)?
Best wishes, Marc