For example, i have 2 parts merged into each other and when i run it they undo, here's a GIF
In roblox studio and when i click play
http://gph.is/2bEg04U
You'd have to create a weld or some sort of constraint to keep them tied together. Alternatively, if you never want to separate them ever, just make them a Union.
You can find out about welds here and constraints here.