The PC-version of AlReader isn't developing now, and it's not compatible with Android-version.
The only way to synchronize the highlights in AlReader to Computer is to install Android-emulator with AlReader app:
1. Install BlueStacks on PC.
2. Download AlReader-apk from official site and run it in BlueStacks.
3. Copy from your Nook:
- the files with books;
- the files .mrk: they only have the information what text in your book must be highlighted (without quick opening the fragment in book with this text);
- the file favorAR.db (from sdcard/AlReader or somewhere similar): this SQLite-database has information about bookmarks.
The path to the books and .mrk files in Android emulator must be the same as on your Nook (or you may edit the paths to books in favoAR.db).
After all, as a result, you have Android with AlReader on your PC (and may be it's possible sync it with AlReader on your Nook with something like dropsync). But it's not look like just having synchronization of highlights to some reader-program on PC, so it's up to you to decide is it worth to do or not.