It takes a long time to paint after
copying
The painting information is saved into the LandscapeLayer info files which you can access in the content browser (and which you can also export and import). So you can directly reapply them to the reimported landscape, no need to repaint.
But yeah, maybe someone can tell you why this is happening, but from my experience something breaks every now and then and sometimes you can fix it, sometimes you can’t (especially corrupted blueprints) and then you need to restore from backup (so unless you’re already doing so, you should make frequent backups, so that you’re not loosing too much of work if something breaks that you cannot repair).