That’s a pain, however I do remember having something similar a few years back, with another NAS solution. I’m sorry I cannot be 100% sure but for some reason I think it was connected to permissions - not just at the SAMBA level but also at the filesystem level.
If it comes back to me I will update here.
EDIT: And just to not help any further (sorry) I have checked a similar thing using my wife’s W10 laptop and it is fine. My laptops are all Linux, and are also fine. Sorry that doesn’t help, but just confirming from my end.
I think this may have something to do with the last windows update because I haven’t seen it before over the last few months.
There was a problem with long files name circa 2018/2019 that required a registry mod and group permissions changes for overly long file names. There were a couple other small items related to Home vs. Pro Win10 versions as well regarding indexing glitches…
Interestingly enough, using a CLI compare and DirCmp app, all the files seem to be there, it’s simply File Explorer is messing up.
This means I can continue to rely on the system as is and not worry about the files counts since Copy/Paste etc. all seem to work as expected.