Tes4Mod:Clean Save

Often a mod/plugin will instruct the player to create a clean save before installing an update or upgrade.  While this procedure may seem excessive, community experience has shown all the steps to be necessary to achieve the desired result of a stable saved game after upgrading.

A clean save is always relative to the mod plugin in question. What it generally means is to remove the mod from your load order, load a save game, and make a new save that does not have the mod in it at all. If you are upgrading, then activate the new version of the mod, load the Clean Save file, test the mod, and finally create a new save containing the replacement.  However, while simple in concept, the devil is in the details.

You should always follow the clean save procedure when you remove a mod, even if not upgrading. Otherwise you may leave behind remnants of the mod that cause inexplicable problems later on.

Procedure
(Assumes you have a good working full save of the game, not a quicksave, which was created with the mod in question active.)

# Load the save game you want to use as the base of your clean save. Wait about 15 seconds after the last message from any mod loading to permit them to finish initializing. Move to an ''interior space, such as a building or cave that is not in any way related to the mod in question. In the case of broad reaching overhauls, the TestingHall may be safest. (See "Notes" below for instructions on accessing the TestingHall.) When in doubt, examine the mod ReadMe and/or documentation for instructions or clues, or ask the mod developer directly in a release thread.
# Make sure you have turned off optional character modes such as Sneak, Auto-Run, NightEye, etc, and removed anything you have stored in containers related to the mod. Save using the menu to a new save game slot.  This is your Safe Location'' save. DO NOT overwrite a previous save slot or use a quicksave. You need this save file to be as clean and perfect as possible.
# Exit the game completely. This is important to ensure you have a good complete save.  Some elements of a game are not saved until the game is shutdown and you don't want to risk that with your save game files.  (There are players with over 1000 hours in their current game who attribute it to always shutting down the game completely before loading any save, among other factors.)
# Backup any INI or similar files for the mod that you may have modified, as a safety precaution.
# Before you touch the mod in question, note it's position in your current Load Order for reference. Both the sequence number, and also the mod name just before it. Write this down; you will need it later. Now either from the Initial Menu (the one prior to being able to load a saved game) or (preferably) from your mod manager, deactivate/disable the mod in question. Do NOT remove or delete any files at this time.
# Restart the game and load your Safe Location save. Wait about 15 seconds after the last message from any mod loading to permit them to finish initializing. Save using the menu to a new save game slot, and then exit the game.  THIS is your Clean Save file. DO NOT overwrite a previous save slot or use a quicksave. You need this save file to be as clean and perfect as possible.
#: You might want to examine your "My Documents\My Games\Oblivion\Saves" folder and either note this filename or rename it (but not the extensions) in case you need to revert back to this point later. Note that if you are using OBSE, there are two files for each save: the game data one with the ".ess" extension, and one with the ".obse" extension. Both are required with OBSE, and must have the same name before the period of the extension, as in "Save 1 -   - Imperial Prison, Level 1, Playing time 00.06.22" before the ".obse".
# Restart the game and load your Clean Save file. This is to ensure it's not corrupted in any fashion before you make any irrevokable changes. Run around enough to cause new cells to load, and test whatever the mod had added to ensure it is gone, then exit the game completely again. DO NOT save again. If the Clean Save is not, restart the process and check your steps.
# Now you can uninstall or upgrade the mod. (Here is where a mod manager that can "roll back" the changes made when you initially installed the mod pays dividends.)
# Read the ReadMe file or documentation for the old version of the mod to understand any additional changes you may need to revert.
#: If you are just removing a mod, you are done. When you load the Clean Save, you should use the "Wait" command until the cells reset (default is 3 days) before moving to a different location. This ensures all changes that may have remained from the old mod have been cleared out 'naturally' by the game engine. Many people don't bother with this "Wait", but it is the safest method. Just recall that impatience now can cost you a lot more time lost later.
#; Continue only if replacing the same mod with an updated/upgraded version:
# READ the new version documentation to determine if you need to replace the old INI file with a new one, or if you will need to make customizations to the new one. Check for other requirements, such as new dependencies upon other mods.
# Install the new version of the mod and activate it.
# Update your Load Order to place the mod in the correct sequence. (Use BOSS.) Most mods documentation will say to "load it last", because this is the most sure-fire way to ensure that mod will "win" any conflicts. Obviously they can't all be last. If BOSS does not recognize the new version of the mod, report what the docs suggest to the BOSS thread so it will get incorporated in the proper order. (Currently the thread is here, but it fills up quickly so look for the link to the "New Thread" link in the last post of each.) Until BOSS is updated either leave it at the end of the load order or add it in your BOSS "UserList.txt" file to the location of the previous version you noted earlier. But be aware that the last position might cause problems for other mods, so you might need to revert to your clean save point once BOSS has it properly sequenced. Fortunately BOSS is updated quickly: once a week or sooner.
# Customize the mod INI if necessary.
# Load your Clean Save game, again wait about 15 seconds for mods to finish initializing, and test the new version every way you can think of. You want to find any problems before you have invested even a couple more hours of your primary game play.
# Once you are satisfied there are not any obvious problems, exit and restart with your Clean Save to re-initialize the replacement mod, and make a new save for resuming play. You want to leave your Clean Save intact in case you need to revert to it again.

Now you are ready to resume playing.

Notes
Check points
It's a worthwhile practice to note and preserve your game at those points before you make mod changes (even 'mere updates' or patches) to your game, or after you have played a significant amount of time between such saves. The basics of the clean save procedure will serve you well, and the Clean Save files themselves make good check points of your game's progress.

Accessing the TestingHall
You will need to perform console commands.  If you haven't already, first read the Console Command Tutorial. You will specifically be using the 'Other Commands' section: 'CenterOnCell BaseID' (CoC BaseID) command.  'TestingHall' is a BaseID.

# Press the tilde key (" ~ ").
#: The game should freeze up as if you paused it. Notice the bottom left corner of the screen has a text prompt window.
# Type the following, which will appear in that text prompt window:
#:: coc testinghall
#: followed by the   key.
# If you did it correctly you will be transported to the TestingHall. Pick a door and enter. (If you haven't been here before, take some time to explore it a bit.)  If you are here to create a Safe Location save, do so now.
# When you are ready to leave, you can again use the console to enter 'coc weye' or any other location for which you know the 'coc place code'; 
#:or
## Exit whatever room you are in, get back to the main, square room.
## Go to the inner square, find and enter the door labeled: "Hawkhaven".
## Once you are in Hawkhaven you may use the fast-travel system to escape.