A chromosomal rearrangement could give you regions of different lengths.

One good way to run liftOver is to do it in both directions, find what maps in both directions, and use those intervals:

1. From hg19 to hg38, taking input A and generating interval set A'

   liftOver(A) -> A`
   

2. From set A', go back to hg19 via a second liftOver from hg38 to hg19, to get set A''

   liftOver(A`) -> A``
   

3. Compare sets A and A'' via set operations, to determine which regions are identical in hg19 space:

   bedopsElementOfExact(A, A``) -> A```
   

4. Run a final liftOver on A''', from hg19 to hg38:

   liftOver(A```) -> A````