I did a initial scan which brought up all IPTV channels in their respective folders. Recently there has been some updates in the M3U file. Some groups were removed from M3U file and the channels have been moved to another group, But even after doing a rescan, the group information is not updated in the interface. I still see the deleted groups in the channel navigator. Is there any way to do a scan from scratch?

You must mark losted channels in scanner report after finish of scanning.

Channels are not lost. They are just moved to various other groups. But in the channel navigator interface I still see them under old group,

Yes, You must regroup list. ProgDVB/ProgTV not do this automatic for keeping groups of users.

Sorry. That is not correct. I found the solution. The grouping option should be changed to 'Provider or Genre' instead of default 'Network or Country'