I want to paint my panels with dp epoxy as soon as stripped to prevent flash rust. Do to scheduling variations it may set in dp for several weeks during the filler work. Is there a problem with just scuffing the dp and applying the filler after the window. Same with primer surfacer. After filler can I just scuff the rest of the dp and spray (urethane) surfacer direct to the dp (and bare metal sand throughs)without reapplying dp over the filler work? Thank you for Help.

You can do all of the things you mention, but on the bare metal areas I would reapply the DP.