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Since you’ll be maintaining the site, at least for now, I’d leave it where it is and do the updates manually as part of whatever maintenance you plan on doing.
Putting the field declarations in the MU plugin folder is a bit of a problem because that means you must have ACF there as well. MU plugins are loaded before those in the plugins folder, actually before some anything else. In order to move it take a significant amount of work, more than likely since you’d also need to put all your code into another plugin and alter it to use the correct hooks for setting up your fields, which I’m guessing you didn’t do since you could guarantee that ACF was loaded before creating your field groups.
Having ACF in the MU folder basically means that updating manually is the only choice that there will ever be, so if you ever need this to not be the case then it will mean a bit of a rebuild.
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