Hi,
We are running out of options...
I don't think you want to run your machine with the flash drive plugged in forever, but that is an option..
Another option is to use Partition Wizard to look at the contents of the System Reserved partition... I don't know how big the "Downloads Folder" is, but it's contents could probably be safely deleted.. That might be enough..
I actually delete the entire partition. Then when I do a upgrade to a new build, Windows usually creates a new one...
Another option would be to try the repair again with the HDD hooked up and "Not Hidden"... Maybe the needed boot files can be found there, since it was hooked up when you installed Win 10 to the SSD...
Something else to check out of curiosity... Look in MSCONFIG at the BOOT Tab... Do you see more then one OS listed ?
I still don't understand why the repaired boot files were placed on the flash drive, and not the SSD... unless maybe they were intended for the HDD and it wasn't there..
One more option I almost forgot about... That would be to try the "Rebuild MBR" feature in Partition Wizard... As I mentioned before, that could be dangerous...
I do remember being involved in another thread in which someone used Partition Wizard to fix a boot problem that was not getting fixed With Microsoft methods... Unfortunately I am unable to locate it for better details...