I thought it would be nice to have all the current guidelines to having a stable modded game along with the ones from previous games that are no longer necessary in one thread. I haven't experimented much with any of these in Skyrim so I'm hoping you can help me fill in the necessary information and I'll update this post accordingly. Feel free to add any other tips or guidelines that you feel belong on this list. Ps: English Isn't my first language so if anyone wants to rewrite anything so that it's easier to read then please do and I'll update the text

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Never overwrite a save game.
Don't use auto saves or quick saves.
If you die restart the game before loading a save game.
Do a clean save before uninstalling a mod.
Updating a mod in an ongoing save game can make it unplayable.
Uninstalling/updating a mod that has scripts CAN make your saves unplayable regardless of the creators instructions.
Programs that optimize textures can cause crashes if used in conjunction with certain mods.