Reliable two-way synchronisation is a complex programming challenge. In my experience the proportion of two-way sync tools that actually work reliably, particularly in common (let alone obscure) edge cases, is quite small. Unison is one of the few examples of two-way sync that actually works reliably.
For this reason my latest leo-based project I have used @nosent nodes exclusively. This way, the @nosent leo nodes are the only "source of truth" for generated file content.
Of course, @nosent nodes can't be used (smoothly) for projects where there are multiple contributors or where it's unavoidable that non-leo tools will be changing file contents.
The reason I bring this up here is I recently created issue
#1450 which concerns what I believe are bug(s) concerning writing of @nosent file nodes.
I suspect that my issue is related to yours, at least in part. See the comments in my issue for further info, specifically the bit about where leo was silently failing to write some nodes.
Cheers