"Up to Date" however certain files are missing!

Yes, hundred times

I think scanner debug logs from Android will probably be necessary to see what is exactly going on here.

On Android, go to the app settings, open the debugging section, then under debug logs enter “scanner”. After doing so, restart Syncthing on Android using the left slide-out menu in the app. Wait for the folder to finish scanning. Then go to Android/data/com.nutomic.syncthingandroid on the phone’s internal storage. You should find a log file there. Please upload it here.

Then as Tomasz asked, please post the path/filename of one of the files that’s missing on the computer but exists on the phone (to rule out invalid filenames).

After that it becomes a bit more complicated, as further debugging would need to happen where the file exists, i.e. the phone. Do you have ADB setup or are able to do so?
Tomasz was faster - debug logging should work too.

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