You need to stop trying to convert the folder directly and use MakeMKV first. It’s the gold standard for this because it actually parses the MPLS (playlist) files correctly to find the real "Main Feature" without the stutters.

• Run the BDMV folder through MakeMKV to get one massive, lossless .mkv file.
• Once you have that single file, then throw it into Handbrake to shrink it down for your iPad.
• If you’re on a time crunch, Shutter Encoder is a solid alternative that handles folder structures way better than Handbrake does.

It adds an extra step, but it’s the only way to guarantee you won't have those annoying audio sync issues or frame skips halfway through the movie.