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Dont Export Flash out of AEFX for this purpose.
Use a more suitable codec for this DI ( digital intermediate)
eg avi, Prores
Is there anyway for me to fix it? I currently can't even open the file that we did the exporting too.
Dont know how to fix something like that.
I suggest redoing it as I suggested above.
Flash is not suitable for that task.
Flash ia a dsitribution codec NOT an edit codec. Just reopen the AE projects and export to Prores or DHxHD or any other "intermediary" codec.
Then import those movies back into PrP to finish your editing.
I'm not sure why you can't re-open your Ae composition.
Be sure to allow enough time for all Adobe background processes
to close before you try to re-open... better yet, reboot and try.
If you still can't open your Ae file, try importing your Ae
composition into Premiere via Dynamic Link.
File>Adobe Dynamic Link>Import After Effects Composition
If you can get the Ae comp into Premiere, you can then do
as shooternz suggests... export and re-import the digital intermediate
to Premiere for further editorial.
And, the "black box" around the "muzzle blast" is probably the background from the Clip used, and you need to create an Alpha Channel to hold that back.