S /D, cd to the previously-hidden system folder contained within $RECYCLE.BIN starting with S-1-5-21, del. To delete the zombie files, I had to go into Command Console in administrative mode, cd to $RECYCLE.BIN, attrib -h -r -s -a. This seems to have been the reason for Merge 2007 failing catastrophically. They became stuck in a kind of Recycle Bin limbo, where I couldn't restore them, but couldn't completely delete them, either. (3) When deleting these super-long file names, the files would go into Recycle Bin but could not be deleted once and for all.
(I have since dialed back the settings to not produce file names so long.) Merge, or possibly Windows itself, was having trouble handling these super-long file names. (2) I had the Cool Utils products set up to export my emails as extremely long file names using the subject, sender, date, and email "nn" code.
Essentially, Linux and Android sometimes will not preserve file time stamps, instead re-stamping copied files with the current time, and sometimes will stay stuck several hours behind or ahead of the actual time zone. (1) The Western Digital ethernet-connected hard drive was running Linux internally, and Linux has a couple of time stamp bugs well documented in the Android world. Upon closer examination, the reason seemed to be three-fold: Sometimes Merge would fail catastrophically and simply vanish from the screen while attempting to compare two folders. There were always a few stragglers that Merge could not copy. The combination of these two changes caused Merge 2007 to no longer be able to synchronize all of my files. These tools allow you to export all of your emails as PDFs and can results in super-long filenames. The 2007 version was working great for close to 9 years until I bought one of those Western Digital RJ45 ethernet-connected media server hard drives, and until I started using 3 tools from Cool Utils called Total Mail Converter, Total Outlook Converter, and Total Thunderbird Converter. I also use it to synchronize my work laptop with a work folder on my home laptop, so that when my work laptop crashes (which it has, half a dozen times already), I still have all of my work-related files safely stashed away. I've used Araxis Merge since about 2006 to synchronize all of my files and folders on my main computer with my USB backup drives.
Extremely powerful software and can be dangerously powerful if you're not careful to pay attention to what you're copying or deleting.