Don't worry, you have not lost any bacteria...here is what I think has happened.
First off...these Autotrophic bacteria are really sensitive to changes in pH. At 8.4 they thrive, above 9 they go dormant, and below 6.5 they also go dormant.
If you are having pH problems throughout the cycling process, which is not uncommon with fluctuating levels of ammonia and nitrate, and then you sorta got it stable for the cycle to proceed, via bicarb. But now you did a near 100% water change and re-added dechlor water and bicarb; what this did was most likely changed the pH a little too sudden for the bacteria and it "shocked" the bacteria and put them into a dormant state. I have had the same problems IME.
I would expect you to see process in a couple of days once the bacteria start to become active again.
Also, one should try to re frame from cleaning a filter until the cycling is 100% completed.
In my sig I made a video on how to properly clean a filter, check it out!
EDIT: The reason the pH fluctuates so much during a cycle is because of ammonia and nitrate; one is more acidic and one is more alkaline, what this means is that these two will pull the pH up and down all throughout the cycling process. And the softer the water you have, the more your pH is going to move around. When I had my tank at my dorm last semester, the pH out of the tap was around 7.5, but during cycling, one day it was up near 8.8, then the next it was down. It will do this until the cycle has finished.
Once your fishless cycle completes and you have fish and everything going, then this is when everything should stabilize.
-FHM