I had the 6.1Gb file and tried to shrink it with this tools.
I was able to process 1250 records and failed with:
modsec-sdbm-util.c:332:dump_database(): Failed to retrieve the next key.
I then move the 6.1Gb file and let mod_sec recreate the file. But I still get the same error when running either -x or -k, on the newly created file.
I tried this on the lastest master branch.