So, I finally have a fix … sorta.
Do this at your own risk and please make sure you have a backup of your database, but on three occasions now for three different sites that have had ACF Repeaters break as I originally described above, this has worked:
1) Export the custom field set from Custom Fields > Tools
2) Delete the custom field set. NOTE: This DOES NOT delete the content that’s already been saved to individual pages or posts.
3) Import the custom field set again into Custom Field > Tools
Now, I did this once on a whim and it worked on my first broken site.
On my second broken site, this didn’t work the first time. So I repeated the process and it did work. I am not 100% sure why or of any differences I did, but now both sites are working fine with new repeaters and old repeaters accepting new data.
NOTE AGAIN: Make a backup of your database! 🙂
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