Hi @combicrux ! - I hope I read your description correctly - When using the Combine command there is an option to "keep tool bodies" one body is designated as Target Body and multiple bodies can be selected as tool bodies. based on your comment you used the "join" option and if from two bodies you were left with one it means that "keep tools" checkbox was left unchecked.
Another recommendation - make sure you capture design history (the file you shared had the design history off) therefore it is not always possible to go back and make use of the parametric design capabilities 🙂
----- let me know if something else was going on -> you can also download the free Screencast app from Autodesk and record your screen + the commands you are running - it really helps with troubleshooting 🙂 -----
please see image for reference regarding the keep tools option- if keep tools is on you will have two bodies in the end of the process - one of the combined bodies and one of the tool that was used:

and here is how to set the document to capture design history (it is best to do so before you run the combine command of the two bodies) :
