As far as I know, sliding a continent around in FTPro is right out. The map elevations are a function based on the fractal function and the lat/long coordinates. Moving it around changes the coordinates. But I have never worked with a burned-in surface before, only randomly-generated worlds.

For filling in the Adriatic Sea, try drawing a selection around it and then setting elevation to 0, rather than trying to paint it by hand. Then you can go through and hand-paint any terrain features you want. You will lose the existing terrain though, so you if you wanted to keep something from it, save off an image and use that image to try and replicate it afterward.

I am not sure using the pre-generated Earth terrain file will do what you are dreaming of though. If I am reading right, you want a map you can zoom in to any piece of and be able to export a clean map, at any resolution. I would be willing to bet (but don't actually know for sure) that the map of Earth is a pixel-based image, and therefore has an inherent resolution limitation. Zooming in won't reveal more detail, just larger pixels. I am trying to get the same sort of result you are, but with a randomly-generated world (see my Gryphii WIP for the project so far). I've gotten as far as exporting map slices that have a 1 pixel = 1 mile resolution at the equator, but haven't yet started assembling them into regional maps, as other projects have bumped it for the moment. You might be able to adapt my work by starting with a flat FTPro world (it's one of the options when building a world) and then using the Pre-Scale editing tools to paint in your continents. You'll probably want to get a copy of the latest beta version from ProFantasy before starting if you haven't already.

Hope this helps, and feel free to contact me with any questions or issues. I'm hardly an expert on FTPro, but I might be able to help, or point you to a resource somewhere.