>>> andy@andy-x200:~/work/talks/2017/icps$ notmuch new 
>>> Processed 230 total files in 7s (29 files/sec.).
>>> Added 212 new messages to the database. Removed 85 messages. Detected 18 file renames.
>>> Error: A Xapian exception occurred flushing database: Value in posting list too large.

I have seen similar "Xapian exception". I don't remember the exact
message. It happens while running "notmuch new" while reading email on
emacs.

> The other generic advice is to run 'xapian-check' to check your database
> for corruption. On Debian and derivatives (e.g. Ubuntu) this is in the
> package 'xapian-tools'.

It found no errors for me.

Cheers,
Rafael