May I ask which inputs produced invalid results for you and which parts you consider hacky? I'd very much like to improve the implementation, so a reply here or an issue on e.g. GitHub would be highly appreciated. Thanks!
Some time ago (~7-8months) I tried to implement a chronofold-based app myself in not so fancy language (c#). The data structure itself is very nicely described in the paper, but for merging strategy there are only references to other papers... So I tried to find it implemented in other langs, most of repos were bare bones, yours was the most complete, so I took it as a reference. I lifted the merging strategy verbatim from it, and it passed all the tests in repo plus some additional tests. But when faced a real user input strange things happened.
I will try to find exact cases and open an issue, but not today, unfortunately :(
Edit: AFAIR, I had problems with this func: https://github.com/dkellner/chronofold/blob/16773193b2d21f81... and the problem manifested itself for concurrent deletes. Plus it has reversed order for consecutive deletes regarding to original paper. I have not succeeded with fixing it and just scratched the whole thing and used a simpler (yet not as performant) merging strategy...
The published version indeed has one bug regarding inserts referencing a deleted element. Maybe that is (part of) what you saw as well. I've fixed that locally already, but unfortunately only after I've made signifant other changes which are still to be refactored & published ;-). Probably time to just backport the fix and release it.