I have a fairly simple model where the holes disappear when I slice it. I've never had this happen with version 4.x.
The model: https://tmp-files-wendt.s3.eu-north-1.a ... unt-v2.stl
Problem in version 5.0.0:
https://photos.app.goo.gl/33EeYqVMNvC3ikpG6
Problem in version 5.0.2:
https://photos.app.goo.gl/bSGcgniTgkxV5S6XA