Say one develops a closed source app that can produce a file of its own format like .ll .Then one asks the user to run a GPL licenced batch script that uses ffmpeg(GPL) to do the final bit. Note that ffmpeg or the batch script is not distributed with the software but install instructions are there in the software. Will the software have to be GPL?
Will the software have to be GPL?
That depends on how closely your software depends on the post-processing by ffmpeg in particular.
If ffmpeg is just one of potentially many (independently developed) programs that can read and process the files your app creates, then your app is a separate and independent work from ffmpeg as far as copyright is concerned and that means both works can be licensed completely independently.
If your app uses intimate knowledge of how ffmpeg works and uses this file format to communicate complex, ffmpeg-specific data structures, then most likely your app will be considered a derived work of ffmpeg and needs to be under the GPL itself as well.
The question as to who invokes ffmpeg (the app itself or the user of the app) I find less relevant. Just the fact that it is two executables is relevant for the determination if the GPL applies.