This is not a full fix unless you were only use a text datatype on your custom metadata. Other datatypes may be set to a zero’d value, like $0.00.
property attributesToScrub : {"Price", "Tax", "Location", "Digital Object Identifier", "Barcode", "Total"}
tell application id "DNtp"
repeat with theRecord in (selection as list)
repeat with thisAttribute in attributesToScrub
set mdQuery to (get custom meta data for thisAttribute from theRecord)
if mdQuery ≠ missing value then
add custom meta data "" for thisAttribute to theRecord
end if
end repeat
end repeat
end tell
Removing it completely would be something @cgrunenberg would have to assess.