Files inside the Binaries/UWPxx/AppX directory are deployed by Visual Studio. It does this based on the {project_name}.build.appxrecipe file, which UBT creates (see UWPDeploy.GeneratePackageAppXRecipe). You’re likely to have a hard time preventing VS from doing the copy as part of deployment, so your best bets would either be to get your self-built binaries into the recipe, or else run without re-deploying.
For the former: easiest is probably to change the definition of XSAPISubDir in OnlineSubsystemLive.build.cs to point at a directory where your dlls live (make sure it’s a subdir of the plugin).
For the latter: make no code changes, build-and-run your game as normal, copy in your edited dlls, then instead of debugging again normally go to the Visual Studio Debug menu, select Other Debug Targets -> Debug Installed App Package…, then choose your game from the list offered.
Note that the cpprest dll is manually loaded - it lives in a path that is not searched by the normal UWP dll location rules - and as such you’re going to have to change OnlineSubsystemLive.build.cs no matter what to account for the ‘d’ suffix. Though I should also say that if you find yourself debugging much inside cpprest you’re probably off in the weeds.