When creating a multi-response/dichotomous the 'base' variables are all kept in the file. So no variables are lost.
There is something to make clear:
+ on the Editing Tab, variables will appear in 'grey' color which also visually helps to identify them as variable used to create a new multi-resp variable.
+ on the Table Maker Tab, all the variables that are 'grey' on Editing Tab are simply not displayed since Designer Mode is conceived as an instrument to Design Tables.
It is possible to transform that 'grey' variables into 'black' ones which on the Editing Tab.
To do this refer to hiding/showing variables solution.