Whenever you are trying to merge some Secondary Level with adjacent Primary levels and you also have the Shear Walls which are modelled as Parametric surfaces in you STAAD Model, then there are chances that Merging can cause an issue. 

The internal logic of RCDC where RCDC checks the geometry of the levels that you are trying to merge may disallow you from merging.

Attached PDF file and Video can provide a workaround to overcome this issue.

Kindly refer the same for detailed clarification -- 

1.  

2. 

3.