It took about 5 minutes to download and install Beyond Compare 5, and also do a quick test. Seems to work very well.
Right now it's churning through all ~350G of the sync folder which it is saying will take about 6 hours. (It compares timestamps, so it's copying a bunch of things that probably don't need to be
Very nice informative intuitive UI, seems to work. If it is as good as it seems to be the $35 will be well worth it.
Don't know why Syncthing & Resilio were so problematic - likely the same issue, but if this works as well is it seems to be I'm moving on.
I've been a nearly daily user of BC since its early days, at least 20 years. There are many useful features that may be less than obvious. I don't mean to be an evangelist, but here are a few examples:
First confirm the BC5 copy is preserving file dates onto your phone. I presume you have already done this.
If you are confident that some files are identical except for their date stamps, then you can use BC5's "Touch" feature to instantly match their dates (you choose the direction). In that case they will not be flagged for copying.
To check candidates for "Touch", select a few representative files and do a binary compare. If binary identical, then I consider it safe to do the Touch on related files.
Occasionally the timestamps will differ by exactly 1 hour due to daylight savings time, or other time zone differences. BC5 has an option to ignore daylight savings time, or time zone differences. It can also set tolerances on the date compare.
BC5 has a special mode for comparing flac files which allows you to examine the plain text tags separately from the binary audio section. This can be useful for troubleshooting file differences.
I use it to keep my primary music storage SSD (as well as Windows document folders and my MC customized app folders), in sync with other PCs and backup drives, both attached and networked.
It has sophisticated comparison modes for spreadsheets.
A model user interface. Good support and active user forum.
The list goes on and on.
Another note: Since you are copying a huge amount of data, you may consider placing the phone's SD card into a USB card reader to do the bulk of the work. Not sure, but it may be faster with the phone out of the loop. When finished, put the card in your phone and access it there for future maintenance and updates (if you are comfortable with the physical handling).
Enjoy!