well, you probably won't get much flavor from the flavor hops as they were boiled for 40 minutes (even 20 minutes is a really long time to impart flavor). Consequently, you probably derived more bittering from those flavor hops than anything. Likewise, you may have extracted more bittering from the bittering hops in the longer boil.
As far as the actual "oops"...you could have added that right at flamout without any problems. No need to boil that additional 20 minutes. As long as it is dissolved it would have been fine.
In fact, the conventional wisdom these days is to NOT boil your malt extract for the full time, just add a bit at the beginning, boil for the indicated time to extract bittering and then majority right at flamout. Again, if its dissolve then its good. Boiling malt extract increases carmelization and darkens the wort.
All in all, it will be fine..