I would hold off on making any plans for a MacOS-based upgrade until CCP releases more info on what the native client is compatible with (from a hardware and software perspective). The MacOS native client is not available yet - we don’t even have a beta date, I don’t think? Follow this thread for news: EVE Online to go native on macOS!
I would make a point of backing up your character and account profiles from the Shared Cache, as that will save having to reconfigure all of your settings later (assuming CCP parses the same core_user and core_character formats in the native MacOS client - which may not be the case).
Anything more would be entirely speculation at this point.
With regard to refreshing your Wine-client install, I’m not at my Mac to verify all the file locations, but I have had good success with running a normal uninstall process on EVE Launcher and then downloading the latest launcher to install again - but I use the CCP-packed-with-Wine iterations.