Thanks for your feedback. This feature was intended for use with lots of short reads where it causes performance issues trying to represent large gaps in this way, hence the split type view for gaps over 1000 bp. However, in your case, performance wouldn't be a problem. So what I've done for the next patch (Geneious 10.0.1) is make it represent large deletions up to the maximum read length (or 1000 bp, whichever is larger) as gaps within a single sequence. Hopefully that should allow you to do what you need. Geneious 10.0.1 will probably be available as a beta version in 2 or 3 weeks time.