I remember years ago, Seb had a command line to recover netcdf files that were not closed properly after a nemo crash (and display zero record but quite a reasonable size for a non-zero record dimension), but have forgot it. Does someone do? My apology if was already posted.
Look at “Can I recover data from a netCDF file that was not closed properly?” in this faq.
However, this was working only for NetCDF3.6.3 or earlier version and XIOS requires that you use NetCDF4… too bad 
Fred, you could try increasing the sync frequency in the iodef.xml
<file_definition type="@{STRINGBASE_xios_ftype}" name="@expname@_@freq@" sync_freq="10d" min_digits="4">
Yes, I tried successfully that option, thanks for mentioning it, Sasha! The last-to-the-crash output was not properly closed unfortunately, but at least I got a few before…