The following is what was output in the command window.

Assertaion failed: (pBlob)->xRealloc==blobReallocMalloc || (pBlob)->xRealloc==blobReallocStatic, file blob_.c, line 170.

This application has requested the Runtime to terminate it in an unusal way. Please connact te application's support team for more information.

drh added on 2009-09-18 21:04:07:
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 c774e298c3f213f7487fb0ba638edfa3f1b89edf. 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.