I was able to get around the error by manually editing the .ldml file (always save a copy before doing this). Note that Paratext should be closed before editing the file. If you have this issue are not comfortable doing this kind of fix, please contact support for assistance.
Part of the data looked like this:
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d/D
d/D
e/E ?/? ?/? e? E? ?? ?? ?? ?? ?? ?? ??? ??? ?? é/É ë/Ë e̱ E̱ ë́ Ë́ é̱ É̱ ë̱ Ë̱ ë̱́ Ë̱́ Ë̃
e/E é/É ë/Ë e̱ E̱ ë́ Ë́ é̱ É̱ ë̱ Ë̱ ë̱́ Ë̱́ Ë̃
+++++++
The issue is caused by duplication of entries. Note that there is also duplication of the ??. Removing the ?? and the other duplications from the file fixed the issue.
TO SAY IT AGAIN - BE VERY CAREFUL EDITING THE FILE.