It depends on how you clean the filter. The water change in itself wouldn't have any effect on the bacteria unless you didn't use dechlorinator. As for cleaning the filter, all you really need to do is lightly rinse (swish it around) in old tank water or a bucket of dechlorinated water (if you've done like I do sometimes and pour the old tank water out before you remember to rinse the filter). I rinse my filters weekly when I to my water changes. You should not experience any mini cycle from a routine cleaning. The one possible exceptin to this is when you change the filter cartridge. In that case, you should let the old and new cartridge run together for about a week and then remove the old one or, if there isn't enough room in the filter for both, hand the old one in the tank near the waterflow for a week or so ntil the new filter develops enough bacteria.
Now for canister filters, that's a little different. I haven't done a cleaning on mine yet so I can't really say on those. If done properly though, you should have a mini cycle there either.
