From what you are saying, the thread title's misleading, the save game files are not missing, if you are at maximum saves, the problem is actually that an existing file was not overwritten, as expected.
The most likely error, is always you didn't do what you thought, if the error does not repeat, you likely failed to save the position, as you thought.
So In the first instance, I'd try to repeat the error, to eliminate user error, as the cause.
I would still suggest you delete the majority of the older saves, AFTER making an Archive copy, rather than overwriting the older ones, as it's always best to keep a full set of saves.
Well designed PC games never limit your saves, we have no need to restrict them, but archiving them, and deleting works for the ones with Consolitus disease.
Out of curiosity what is the max saves limit? I currently have 71 manual save files.
It would also be very prudent to check the Savegames folder and files has not been set to read only in windows, by checking the folder properties window. Games will often appear to save as normal, but it never gets applied to the file if the read only box is ticked.
I've found this is the biggest cause of most saves missing reports, but probably not in your case, as it's usually all saves missing, and often the settings as well.
Folders, only shows two possible outcomes
Box ticked = All files set to read only
Blacked out box = Less than all files may be set to read only. (Range is zero to All-1)
Files results, has three outcomes
Box ticked = All files selected are set to read only.
Blacked out box = Some of the files selected are set to read only.
Box empty = None of the files selected are set to read only.
Rather than check each file individually to find the ticked files that are set, you can select a section, to narrow things down quicker, with halving each time being most efficient elimination process.