Here's my understanding of how it works and a way of thinking of it that might help:
Think of the map-room as an object that needs to be "destroyed" to capture the base. Each uninjured troop that gets in to the maproom, when it is white flagged, does 1/10th of the necessary damage, so it takes 10 troops to "destroy" (capture) the map-room.
1. If you had say five troops enter the map room safely and lets say the other five where shot. If you re-up before the base is captured to run another set of troops, will re-uping kill the first five troops that made it safely into the map room?
No, re-upping does NOT change the fact that 5 troops already made it to the map-room and "damaged" the map-room 50%. It will stay 50% damaged (only require 5 more troops to capture) as long as it stays white-flagged. The only way that "damage" from your first five troops goes away is if the map-room goes back to a red flag. When the map-room goes from white flagged to red flagged, you can think of it as back to 100% undamaged.
2. Lets say you let all ten troops go on a long run to the map room then your trusty M3 is killed. Will the troops die if they have not made it to the map room and you re-up?
Your troops will continue to run even after you die (or exit), the same way bombs continue to fall or torpedoes continue to run after you are killed or captured --
so long as you DON'T re-up before they reach their target. If you re-launch, anything you released last sortie (troops, bombs or torpedoes) will go away.
Hope this helps.
