I am using Cubase Pro 9.5.10. I have the preference Replace Recording in Editors set to Controller. When I am recording MIDI data and have the MIDI Record Mode set to Replace, I expect that the only data that will be replaced is continuous controller data. This seems to work for a short time, however, after two or three times it seems to revert back to replacing all the MIDI data. If I go back into Preferences and look at the Replace Recording in Editors setting it is still set to Controller. Sometimes I can play around with setting it to None and then back to Controller and that will make it work again but it’s not consistent.
Could you try in Safe Start Mode (after this, you have to adapt your preferences > Record > MIDI > Replace Recording in Editors, of course), please?