UNTIL NOW...
I discovered a very easy way but I really think there should be a better way. Maybe you can do this better in older versions.
All you have to do is arrange the clips together on the time line.
Go to Produce section. Select MP4 and then press Start (I did MP4 but I suppose other options might work)
This takes a while to render. Once it does go to Edit section
The MP4 clip you just created is now in the Library
Select and drag it on to the time line.
You now have a clip that includes all the clips that you couldn't crop at the same time.
Now you can crop the whole new long clip at once.
If someone knows a faster way, please post it.
Thanks!