There currently is no proper way to join/merge/unsplit clips that have been altered after splitting. This is a serious deal breaker for me, as it makes working with clips REALLY inconvenient, even though i know that there are ways to work around that. But why make it complicated if you could make it simple?
A clip is a subset of sequential frames from a source media file, it is represented by an start frame and an end frame.
source = 1 2 3 4 5 6 7 8 9
clip1 = 2 3 (start = 2 , end = 3)
clip2 = 4 5 (start = 4, end = 5)
clip3 = 7 8 (start = 7, end = 9)
clip1 & 2 can be joined to a new clip = 2 3 4 5 (start = 2, end = 5)
clip1 & clip3 can not be joined because it is not a sequence with a start and end frame.
What you is thinking about is clip grouping, there a number of clip can be locked together and handled as one clip, shotcut don’t have groups support currently. but is on the roadmap
one workaround in shortcut is creating a sub project in a separate .mlt file and insert that as a clip in the main project.
another way is to export (render) the clips using a marker into a new joined video clip and use that in your main project.