Every time I download an installer or run a major update, the executable restores the afcad to the original version.
It doesn't do only that. It also makes a BACKUP of the AFCAD that was originally found installed, if it's not the same version that is online. This is obviously made intentionally for the one and only reason to preserve user-edited AFCADs.
The backup is always made in any case, regardless of time/dates of the file found on your system: IF your file is *different* (the check is made with MD5 hashes), it will be backed-up.
I lost all my updates to PHNL because I hadn't backed it up
No, you haven't, unless you removed some files yourself, not realizing a backup was made.
The back is named with the time and date of the installation date appended to the original name, so there will be a new backup each time you run the install so, no chance to lose a file. The file is named with a .BAK extension, so it won't interfere creating an AFCAD duplicate, but is still there.
However, adding such an option would make a significant difference in having to maintain the afcad file after every update
Since the installer makes a backup, there's no need to do anything, if you don't want to use the most updated version, simply rename the backup the installer made for you the same as the original FSDT AFCAD