Yes, this is a challenge.
Graphics mods (map, icons, photos, etc.) are modded in the main game folders, so they will persist after an update to the game. You just need to uninstall via JSGME, patch the game, then re-install your mod.
Changes to scenarios will need to be supported through the life of the game, possibly like this:
1. Save your modded scenario with a unique name. I call mine things like dc2scenario1_PZKRG_1.0. This ensures that a patch will not make any changes to your mod version.
2. Depending on what the patch introduces (you will need to really study the patch list, forum posts, etc.) you might need to:
2a. Open the new patched Vanilla scenario and import your map, SFTs etc., or;
2b. Make the same changes inside your modded scenario, e.g. by importing new events, importing the patched map or units and so forth.
It will require commitment and you might need to repeat a lot of tasks. Once the game stabilizes, this issue will largely go away, so I would suggest that you focus on smaller mods and small scenarios for a while.