I can't offer you any advice on keeping your game clean, hopefully someone more knowledgable will help. I can, however, tell you that the cell reset occurs after 10 in-game days for regular cells and 30 days for locations marked as cleared. The problem: you can't enter the cell during this time or the counter will go back down again. I'd recommend waiting 30 days (or 31 for safety, wouldn't wanna accidentaly miss a day and ruin the reset

inside your own house and then checking if the bodies cleared up.
On a side note, do you use any mods? It would be a good idea to install the unofficial patches, I think they fix whatever cleaning issues were left out in the official patches.