Nothing as elaborate as that.
When files are copied into the AUTO folder, the entries for each record starting from 1st to last entries are read and executed (if it is executable, non-executables are skipped). It does not re-sort according to datetime nor alphabetical or anything like that. As you copy files into the AUTO folder, it just fills in the next available records.
So if you delete a file in AUTO folder that occupied the 3rd record (and executed as 3rd order when reboot), you get a "empty slot" in record 3 and if you copy another file into AUTO now, it will be placed in that 3rd record. So that particular file you just copied will be executed 3rd in order.
The records mentioned above are the FAT entries. FAT = File Allocation Table.
You can effectively change order of booting PRG this way. Of course as Leech mentioned, using AUTOSORT would be a better way.