OK, figured it out...problem entirely on my side and caused by my lack of understanding of the JFS configuration and it's pre-requisites.
Sooo...I moved from an all HPFS386 configuration to all JFS. To accomplish this I relied on a maintenance partition (where I executed the XCOPY from), which was configured by default to run HPFS/HPFS386 and to which I added (key point here: MANUALLY) the JFS capability.
Well, if you've done some JFS work by now you might be screaming at me: "HEY, SHMUCK, YOU FORGOT ABOUT \LANGUAGE\* DIRECTORY!". Yup, that's what it was.
The presence of the DEVICE=G:\OS2\BOOT\UNICODE.SYS statement before the JFS driver in CONFIG.SYS is a requirement to running JFS. Well, since I manually retrofitted JFS to my maint partition I had also included this statement, however what I did NOT do was to move the \LANGUAGE directory tree over. This meant that UNICODE.SYS was loading but showing some warning messages...which in hindsight I should have investigated further. In reality UNICODE.SYS was not actually loading successfully at all, in fact the reference to "\landugage\codepage" is actually hard-coded in the driver itself and since that whole directory tree was missing from my maint partition there was an impact to JFS operation.
However, since I was able to format JFS, execute XCOPY, run CHKDSK and in general use JFS just fine I had assumed that all was good. And so this is how I copied my HPFS386 based stuff to the JFS system.
Now given guzzi's hint I went back to review all this further and learn a thing or two about UNICODE.SYS and OS/2 CODEPAGE functionality. I re-formatted a test partition and having moved the \LANGUAGE tree over to my maint partition I did the full XCOPY of my OS/2 drive. Once up and running I ran WCD against it...and...SUCCESS!!!
I repeated this process on my main partition (SSD drive) and so far I'm all good. Now, does this mean I may have lost some type of information in my previous XCOPY from the HPFS386 system??? I do not know...CHKDSK always reported matching file and directory counts, although EA numbers were somewhat different.