That would be unusual. Occasionally the "now and next" has different data to the x-day guide, but you shouldn't see a difference on listings several days away.
The other thing that can happen is you have merged channels, such as an CBeebies HD and CBeebies (SD), and they have different data; but merging HD and SD is a bit difficult to do in 4.2.8. I'm assuming you only have one DVB-T/T2 tuner, not merging with satellite, and that tuner is only picking up from one relay.
I don't think 4.2 has any filtering for "fixing up" listings, since I only introduced that in 4.3.
You checked that the service was definitely stopped before removing the db?
Assuming no merged channels and only one EPG module then it shouldn't do that. A lot of changes have been made in that area in 4.3 so it's probably it's already fixed in there. If you choose to upgrade, then you should do a backup since the on-disk formats have changed.