Ok so this is a strange one. When I use an external editor with Lightroom, when the file would come back the original and externally edited ones would read 1 of 2, 2 of 2 now I don't see that anymore. Can it be turned back on?
Assuming your image versions are being stacked - and have been in the past - it may just be that these stacking indicators are not showing for you.
This easily happens (unintendedly) with the Filmstrip, when that is reduced below a certain height and its thumbnails become too small to sensibly show info badges. Even if the LrC view options say they should be shown. Enlarging the Filmstrip will in that case show these badges once more.