I think I'd take a far different approach to this task, though one that might prove to require a little more work.
If they are actually going to be involved/interacting in the flashback, you really have to set it up more like you would a time-travel type of adventure, IMO.
I'd make sure that I took stock of the individual character's significant accomplishments...maybe three or four for each one. You might even have the players make this list prior to the session.
I'd set up the game so that what is happening in the present reality has a significant goal that must be achieved...and part of that goal by each of the characters.
I'd then start the game in the present and get them started on their goal(s).
Then in the first flashback, allow them to gain some knowledge that will help them in the present.
When back to the present, if someone has died in the flashback, adjust the present based on that list significant accomplishments. This might even include losing another character if their life was saved by the character that died in the flashback. Inform the players that in the present they no longer are aware that the dead character(s) had ever existed and need to continue based on that lack of knowledge. Change their goal(s) or reassign them based on the who is left alive.
In the next flashback, take it to a time prior to the last flashback and give the players the chance to save the character that died in the previous flashback.
When they return, again, to the present, and if they have succeded in saving the characters that died in the first flashback readjust the goal(s) and inform them of the new adjustments to their knowledge base (perhaps even including some things that are "now true" that weren't when the game started because of the odd changes that have happened.
Each flashback should include possible dangers and information to help them in the present.
Could be tricky, but if you aren't going to use flashbacks as "narrative-only" additions to the game, you truly have to include options and consequences...or they aren't really interacting...they'd only be following your scripted version of what will happen regardless of their input.
*shrug*