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That's probably where the issue happened. Your migration extension may not have transferred the data correctly.No, it was installed new on a new J3.1 site and data sucked across from J2.5/cb1.9.1 with SP transfer because advertised Joomla upgrade just did not work.
Removing the duplicates shouldn't cause any issues as the fields are stored to _comprofiler by name and not ID. It could cause issues if those field ids are stored to anything though like in CB Conditional usages, etc.. so you'll want to ensure the newest duplicate is the one removed instead of the original field. Be sure to also run CB > Tools database checks after removing the duplicates.Manual removal of the newer duplicates in_comprofiler_fields works, but I have to check that nothing is lost.
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