Since the alignment is not out by a great deal, you should be able to time-stretch or time-shrink your BIAB wav file to match with file in Cubase.
I use Reaper and in a situation like this, what would do is... align the left sides of the two tracks. I then go to the right end of the file I want to stretch/shrink, press and hold CTRL+ALT and drag the end of the faulty file to match the other file.
Regards,
Noel
Spot on Noel,
I did, essentially, this in Reaper today: I'm working on an old song that a) has a decimal tempo & b) has a ritardando section.
I lined up the beginning created splits where the tempo really became OUT and used Alt with the mouse to stretch/shrink the sections L&R of the split .wav file. It only required a couple of splits for the general tempo though rather more detailed work and aligning to get the slow down sorted. It was worth the effort as I now have a very fine gospel style backing vocal that has a "great Gig In The Sky" feel thanks to BIAB.
Working with BIAB out side of the program, until they down tools on the money making updates and focus on the core issues, is always going to be a work around.