I suspected this problem too based on conflict resolution results, but after actually running tool from here:
py git-filter-repo --analyze
stats in the output file .git\filter-repo\analysis\blob-shas-and-paths.txt
are something like this:
=== Files by sha and associated pathnames in reverse size ===
Format: sha, unpacked size, packed size, filename(s) object stored as
1 4fdc4b7d67 152745 33950 FluxFilter.json
2 0f3485f0f5 151344 16160 FluxFilter.json
3 addd4890d5 129822 13719 FluxFilter.json
4 369c158d9a 142178 9915 FluxFilter.json
-----------------------------------------------------
17 1112b3b1e5 124947 4283 FluxFilter.json
18 1f24aa6fc3 116120 2147 FluxFilter.json
19 33082e1551 126083 1758 FluxFilter.json
-----------------------------------------------------
20 a8b634d405 130377 1329 FluxFilter.json
21 9346666842 130426 1300 FluxFilter.json
22 e7895f6751 137863 1253 FluxFilter.json
-----------------------------------------------------
26 6aa197cf49 115980 627 FluxFilter.json
27 8a6ba2124e 135864 589 FluxFilter.json
-----------------------------------------------------
41 c27fad51a2 146322 191 FluxFilter.json
42 d6227db139 149838 189 FluxFilter.json
When compressed file size should be around 30000. Which looks like sometimes git handles changes correctly and sometimes fails.
As suggestion attempt: possibly check with this tool if JSON to blame or some other file?