Unfortunately there is nothing you can really do about this. One of the effects of deleting fields as you've discovered is to mess up scripted imports. Instead of deleting fields from your database schema you could just stop using them - take them off layouts etc, but not actually delete them. If they are calcs that are slowing down performance just change them to text fields. By not deleting them you don't mess up your scripted imports. The other option is to reset all scripted imports after doing field deletions. You should also consider what happens to scripted imports when you have added new fields also.