Solved my own problem. Here's how...
This project involved several trips to the jobsite in various stages of construction. So I had dozens of scans from at least 15 different locations. All I was worried about for this latest trip was some bolts I had scanned for an as-built - needed to locate them exactly within the scan. I didn't need all the earlier scans from weeks past in my way, so I went into the Project Explorer and rather than simply toggling their visibility off, I deleted them. This was bad. It seemed logical because I had already completed my work with those scans in weeks prior, but they were still in my data collector for this same job so they came in (again) with the JXL file, dragged-n-dropped into TBC into a new file.
Obviously simply deleting the older scans did more than just delete them. It affected my Raw Data, points from resection, and some other things I probably still don't know about within the file and data structure. I still think it was weird that I could see the "missing" data points during Scan Registration, but at no other time.
I started with a new, blank TBC file. Then dragged-n-dropped my entire JXL file from the data collector into TBC. Then, rather than deleting the older scans I didn't need, I went into the Project Explorer and toggled off their visibility. I still had (visible) the (3) scans from the recent site visit that I needed to work with. One from a resection location, and two more scan stations that needed to be registered. I performed scan registration as I normally do and got a good result as expected. Since the old scans were still technically in the file (yet not visible), I had to be careful not to attempt to register them. Be sure of which scan you're registering if you don't need to register them all - aka unnecessary data. As in the problematic times before I could still see my "missing" data during Scan Registration, so I didn't really know this had worked until I finished registration and dropped back out to Plan or 3D Model view.
Well it DID work. Not only did I have my "missing" data... I also had my Raw Data back as well. When I wrote the post above I was so frustrated, I never even noticed I was also missing my Raw Data - the green lines between scan locations, and resection points, etc. I was just so focused on the missing data and getting it visible.
Anyway, I hope this helps someone. If you don't want a scan in your TBC file, but it comes in with the rest of your data, don't delete it. Just toggle off it's visibility in the Project Explorer.