Glycogen is maintained and replenished during ketosis.
I was doing some reading and stumbled across this rather old, but very interesting paper. The idea is simple: they put rats on a ketogenic diet (surprisingly, real meat and vegetables) and had some train (running) and some not. Liver and muscle glycogen were examined before and after exercise (running). Here is the key for their abbreviations:
TE: Trained experimental. Ketogeneic, running program for previous week, running during experiment
TC: Trained control. Ketogenic, running program for previous week, not running during experiment
UE: Untrained experimental. Ketogenic, no running for previous week, running during experiment
UC: Untrained control. Ketogenic, no running program for previous week, not running during experiment
The block in the upper left corner shows the time where exercise is occurring. Everything after is recovery.
Figure 1 is ketone levels, 2 is liver glycogen and 3 is muscle glycogen. Clearly glycogen stores can be replenished during ketosis after exercise, and having been on an exercise regimen makes it happen for efficiently.