I'm not sure what the OP means by the sentence: "I used checkout to try to only
checkout a specific file...."  But I did observe that little error checking is
done on the "checkout" command and so if you give it the artifact ID for
something that is not a check-out, it will not give a reasonable result and
will often segfault.  That defect, at least,
has be fixed as of check-in But
it is unclear whether or not that will fix the OP's problem.

We do see clearly that the "checkout" command will not modify any files in
a check if those files have changed in any way, unless the "--force" flag is
used.  So I do not thing the OP lost any work.  All the deleted files can be
recovered simply by doing a "checkout" of the version that was in the repository
prior to the failed checkout.