Quicktime XDCAM rewrapped to .mov showing offline media in some clips
Currently using Mac Trashcan with OS10.12.6,

Premiere "Pro" 12.1.2...but this issue has been occurring since the 12.1 release...
Just to give you background, I have been editing our show ("Chicago's Best, on WGN/Ch. 9 in Chicago) for 8 years now, cutting well over 250 half-hour shows. We've gone through FCP6, FCP7, and now the various iterations of PProCC.
Previous to conversion to an all Adobe workflow this year, we would import and re-wrap the MXF files generated by our Sony F350 and EX-3 cameras (via Sony's XDCAM Transfer program), creating Quicktime movies for edit. This was not a problem at all...UNTIL the dreaded 12.1.x "update".
When creating the master timeline, we have a tease segment which uses clips from previous shows, and I need to open the older projects to create a "clean and dry" version of the old segment for that tease. I'm having a hell of a time getting 12.1.x to properly open PPro projects created in earlier versions of PPro.
Frankly, I'm not sure why this is happening at all. Let me show you why I'm confused with some screengrabs to illustrate my issue.
Since the blasphemy that is the 12.1.x update, here's what I get upon opening projects containing QT XDCAM media:

This is the timeline for the segment I need to export...you'll note that many (but NOT ALL) of the clips are offline. Let's zoom in a bit to examine the clips more closely:

No big deal, right; PPro has strong re-linking tools, I'll simply Link them:

So I "Link Media"...and yup, that file is there...only when I select it, I get this infernal message:

UH-OH!!! For some reason, and quite randomly to my best guess, PPro thinks that that file I want to relink DOESN'T HAVE VIDEO! Now, look at the timeline again...you'll see that some clips are linked and some aren't. THERE'S NO DIFFERENCE, TECHNICALLY, BETWEEN ANY OF THOSE CLIPS! The clips that link properly, and the clips that don't, were ingested via XDCAM Transfer using the same settings. Yet PPro sees some difference here.
Here's what out VideoSpec utility says about the "unlinkable" file, and a file that links OK. First, the "unlinkable"":

...and this, which opened and linked just peachy-keen fine:

Except for the Creation Date, and a tiny difference in the "Bits/(Pixel*Frame) ratio",, they're identical. But not to PPro.
Of course, I have a workaround, and that's to open up the unlinkable clips in QT, save them back to the same location...and THEN, Premiere will admit that yes, they DO have video, and I CAN Link them. And while this is fine...for one segment...I have, literally, THOUSANDS of files with this potential problem.
This is a stupid way to run and "upgrade" an editing program. Anyone else have this trouble? Anyone else got a fix?
Moderator note: changed title to reflect issue more closely
