I face many years same a mistake.
When replacing of the existing file in PDM (it is unimportant with what extensions) the message - "not recognizable formatting of the file" appears.
At the same time, practically always I at the same time have opened (but not active) a PDM Explorer window in which this file is selected.
If to remove allocation of this file (to select any other file) - the problem disappears.
As I understand - a problem in some blocking of the file, it is possible because of some PDM or Windows settings.
I also had suspicions on - Workflow - "ignore permissions in the previous states".
But in that case, I think that at removal of selection from the file - nothing would change (perhaps I am mistaken).
The problem is that forcibly it is impossible to recreate a situation and when it occurs - there is no time to deal with it.
I see that there are similar questions, for example - https://forum.solidworks.com/message/875023#comment-875023, but decisions do not suit me.
Whether there are still some offers?