It happens all the time and the only solution (when editing a LR file with PS and importing it back to LR to make sure I keep the altered file) is to manually save a copy to a new PS folder. It's bothersome and I know this isn't how I should have to save my files.
When I want to edit a LR file in PS I press command E
I select the first option, edit copy with LR changes
I do my work in PS
I either select Save from the file menu or click to close in the upper left hand corner
I get the prompt to save the document, I select yes
I go back to LR and it's there -- most often, but not always, as a second copy.
Here's where things really go wonky:
I create a virtual copy in LR and send either one to PS
I edit in PS and save it back to LR
BOTH copies are changed.
In PS I create a duplicate of a file from LR
I save both to LR
LR saves whichever version I closed/saved last, overwriting any duplicates I made in PS.
This is driving me nuts.
I've gone so far as to shift, option, command at PS startup to clear the settings, but it didn't work.