That didn't help. I ran the permissions repair, but none of the Parallels permissions were at wrong. They all had something to do with photographs I took, not any system files.
I think the problem is that prl_disk_tool is actually in the Parallels Desktop.app package itself. I opened the package and found it under /Contents/MacOS. Opened SecureCRT and went to that directory and ran it as ./prl_disk_tool <etc> and it worked.
I think.
I can't tell if the old snapshot (month and a half old) merged or not, but it was still there as a file and disappeared from the Snapshot Manager when I deleted the snapshots.xml file.