Note
Consider the implications of removing a mod from your save game in this manner. When your game loads such a save, it may find that some things don't make sense or that there are references to things that don't exist, and this may cause issues. Pure UI mods are likely fine; AI mods or mission mods will probably cause minor or temporary problems; and major additions like new ships/equipment/sectors really should not be removed on a whim.
Finding the save files
Open the file browser and navigate to this folder in your My Documents folder:
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Egosoft/X4/<numbers>/save
Decompressing save files
If your save files have the .xml extension, you can skip this section - but by default (savegame compression is on), they will be .xml.gz files. To compress and decompress save files, I use 7Zip. Extract the file using any appropriate program, so that you now have a .xml file.
Editing the mod out of the save file
You'll notice the save file is extremely large - this is why they have compression on by default. In my experience, Visual Studio Code is a great tool which can read and search through these massive save files without breaking a sweat. Opening the file, look near the first few lines, or do a ctrl+F for the word "patch". You'll see something like the following:
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<patches>
<patch extension="MeJ_Improved_Explore_Behaviour" personal="1" version="51" name="Improved Explore Behaviour"/>
</patches>
You can compress the save file again, if you like. Back up the original .xml.gz file, and then replace it with this one, with whatever program, using the gzip format.
Finishing up and other notes
Now the game should not refuse to load this save.
If it doesn't have any effect, and you have the Steam version of the game, it could be that the cloud sync support in the game is overwriting your changes with the older versions. Consider disabling cloud support for X4 temporarily and repeating the process.