I would have the upgrade option on the exotics lock them at 300 damage with just the 3 end damage upgrades reopened for levelling to the new dmg levels so you lose nothing by upgrading. If the item wasn't fully levelled before then have the same amount of upgrading left to do before you can start levelling to the new dmg levels. Same with armor. Just reopen the last line of upgrades to take it to the new levels.