Just run into this problem and it’s a pain. Wish it notified when applying ANY sort of processing.
Not quite sure this post offered a solution to address the issue in batch PRE import. Seems like the only way is to fix it is after import or make sure a particular metadata isn’t embedded in the file.
In my case I noticed an incorrect samplerate that mismatched that of my project. Cubase then rather than ask me to convert the rate just applies audio warp. I now enabled the setting to convert automatically on import. Hopefully that should address my particular issue. I also made sure that ‘Align to Project’ was disabled in the Mediabay as it’s an easy one to miss and then scratch your head after when something sounds off.
I’m Cubase 7 btw. Maybe this was addressed in future versions/updates with a simple pop up on import.