Help! When deleting unused variables, moving assets in master slide layer.

Hello All 

I am having some issues deleting unused variables on a blank template. 

I noticed things moving inside different states on a master slide layer at some point during design, so I went back to the start to look what was causing it. 

I found the issue, when deleting unused variables, when I click OK, the variables delete, then everything on the master slide layer moves. 

Nothing on this layer is connected to the variables that are being deleted, they are unused after all! Also all the items that are changing are locked to prevent movement.

I did manage to get it on video as I was making changes step by step to make sure I could determine what was happening

Any ideas on how to prevent this, other than not deleted the unused variables?