First and foremost, uninstalling any kind of mod mid-playthrough is considered bad practice and may break/corrupt your savegames. Some mod authors and users spread the myth there's something like a "clean save" you can achieve in specific ways. But that's just a myth. Uninstalling a mod will always leave broken references and/or altered data in your save and there's no way to reliably remove or fix them all. In some cases they won't do any harm in others you have a broken save you can't progress any further a few hours later on.
If you want to learn more about this topic you can find a lot of information here: https://steamcommunity.com/app/489830/discussions/0/1520386297681801135/
The authors mention Skyrim but all of that applies to Fallout 4 as well, it's the same engine after all.

Even with all the precautions outlined below there's no guarantee for a bug-free experience. This is just based on the feedback from people doing this kind of procedure who didn't notice any issues. If you still want to try to switch from another mod to ECO mid-playthrough here are some steps to increase the chance of getting a working setup after the transition:

• Load your current save with your "old" mod setup.
• Create a new hard save. This one will be used later on if any problems arise.
• Remove everything contained in the mods you want to uninstall from your character and settlement containers (e.g. workshop storage) by selling those items to a vendor and/or using console commands.
• Wait or sleep for a couple of in-game days after selling the items - 5 should suffice.
• Create a new hard save and quit the game.
• Disable the mod you want to be replaced.
• Load the save you previously created.
• Save again to a new slot and quit.
• OPTIONAL: Download and start ReSaver (Fallrim Tools), open your most recent save with it, check and fix any errors, unattached scripts, etc. and save the modified savegame in new slot. This should be used with caution. No automated process is perfect and it can lead to removing too much savegame data.
• Install ECO and start the game.
• Make some tests with your new setup before continue playing.
• If you won't notice any problems you can stop here and have fun with ECO's features. Otherwise disable ECO, reenable your previously disabled mods and continue playing with the first save you created for this guide