Multicam edit with once source needing global fixes. When and how to do it?

First post and new to Premier Pro from FCP. Be gentle, as this is not simple to explain much less understand.

Three cameras shot, one was SD so I uprez it using Boris Instant HD. I do this by dragging the SD footage into a sequence, adding the filter and then making it a nested sequence. Next, I put all three cams in a multi cam edit so I click HD footage 1 HD footage two and nested sequence and make a multi cam edit. It work. Is that the best way to edit in multi cam with a clip that needs a "global" fix before you even start or edit native then add effects later. If I do that I might have to add my HD uprez filter to 40 clips?

The real problem arises when I use parts of the SD footage for b-roll. To be clear, I select the original SD footage, not the uprezed sequence and take a few seconds from it. Then return to my multi cam sequence and the two HD cams are present but my sd to hd nested sequence seems to have taken the edits from my b-roll and it gone.

My questions:
-Better ways to fix "global" changes before going into Multi cam?
-Where is my previously un-affected Multicam sequence with my Nested uprezed sequence?
-Finally, a bonus instead of starting over how do I get it back? It goes black in the spots where my nested sequence was. Like I could simply connect the footage but it is there as I hear audio from it.

Of course I truly appreciate any help as I know this is an intrusion into your time.