I would say that is some of the problem if not the root
Overfeeding can lead to this as you may have been aware since you stopped but since the food is still down in the gravel/substrate it will cause nitrates to go up. This is why its important to vacuum the substrate. The next water change you do and everyone after I would vacuum the substrate the best you can going all the way down to the bottom. This will reduce the nitrates as it will get the uneaten/waste from the fish out thus helping the overall water issues.
Having the filter down for a couple of days might have contributed but I think the main cause is not vacuuming/overfeeding.