When adding or removing mods from Skyrim you'll often be told to "wait 30 days for all of the worldspace cells to reset". The classic example of when to use this is when you've removed an armor mod, and found that half of your NPCs are now wandering the cold of Skyrim naked!
Alternatively, sometimes you'll just want to reduce the size of your save by waiting for all the cells to reset and be removed from your save. This is how to do it without waiting a month in game time.
NOTE: Bear in mind that this process will reset every hostile area you've cleared, so don't be surprised when the bandits move back into camp the afternoon after you spent all morning clearing them out!
Step 1 - Check the current setting
You'll want to get the current settings for the cell respawn timers. There's two of these, and they work in tandem, letting the game count down the number of in-game hours before the cell is reset. Since these can be changed by some mods (like SkyRe, PerMa, or Requiem) you'll want to check your specific settings first.
You can get this information by writing down the results of the following two console commands:
For me, these numbers were 120 (five days) and 288 (12 days). Make sure you make a note of which is which!
Step 2 - Set for quick reset
Then you'll want to set these settings so that all of the cells will reset within a single game hour. You can do that with the following two commands:
setgs iHoursToRespawnCell 1
setgs iHoursToRespawnCellCleared 1
Step 3 - Wait a couple of in-game hours
...just to be sure. Use the standard wait menu, or just hang around and let time pass!
Step 4 - Reapply the original settings:
Set the settings back the way they were before you started, by reapplying the numbers you wrote down in Step 1 using the same commands. So for me, the commands would be
setgs iHoursToRespawnCell 120
setgs iHoursToRespawnCellCleared 288
Then save your game
All done! If things like naked NPCs persist, then you now know it's most likely down to miss-assigned armor meshes or body slots in a mod, but it's not down to the mod you removed! You should also find your save sizes are considerably smaller as a result!