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In my case this had to do with a mismatch between the database version and notmuch version (notmuch was upgraded but the database wasn't). A quick notmuch new fixed the problem (you need to close and reopen emacs). YMMV.

ychaouche@ychaouche-PC 14:52:57 ~ $ notmuch new
Welcome to a new version of notmuch! Your database will now be upgraded.
This process is safe to interrupt.
Backing up tags to /mnt/partage_local/DATA/MAIL/backup-fetchmail//.notmuch/dump-20170917T135312.gz...
Your notmuch database has now been upgraded.ining).          
Processed 20 total files in 2s (6 files/sec.).
No new mail. Detected 20 file renames.
ychaouche@ychaouche-PC 14:54:56 ~ $ 

As you can see here 20 filenames have been renamed and the notmuch new command seems to have correctly detected and fixed it.

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contact : @ychaouche yacinechaouche at yahoocom