My iMac will not sync all photos to my iPhone

I have a very similar problem to some already mentioned on here when syncing images from my Mac back to my iPhone. However all the suggested fixes I have seen refer to iCloud. My issue has nothing to do with the iCloud because I am connecting my iPhone to a USB port on the Mac.

After taking photos with the phone I carry out the following operations:-

Use Image Capture to download images from the camera roll (or whatever Apple want to call it now)

Use the Exif metadata editor to prefix all the image names with the date taken in yyyy-mm-dd format so that any images sent to my phone by other people are in the right sequence and get sorted appropriately.

Separate the images into folders based on the year.

Sync the all the folders back to the phone and clear out the camera roll.

I have been doing this for many years and never noticed a problem. There are now just over 11000 images in the folders. Recently the sync process asked me to delete all photos on the phone before doing the sync.

I then noticed that the image count in some folders did not tally with the count on the Mac. Out of curiosity I did the sync again; this time another 2000 images were copied to the phone. But some folders still did not tally. I tried to sync a third time but no more images were transferred.

A supplementary question is why is all this syncing and backing up of phones and tablets done through a music app and not a completely separate app?

Thank you for reading this far.

[Re-Titled by Moderator]

Original Title: Mac will not sync all photos to my iPhone