I know they are normal folders, but have you even tried to use SkyDrive to link a folder underneath folders with .bc extensions?
Like I said, if you tried, you would know why I had to unregister boxcryptor from .bc extension before linking it to SkyDrive. Under Dropbox, it allows me to manually type the encrypted directory path, otherwise, just from mouse and UI alone, you wouldn't be able to select the encrypted folder under .bc extension.
Hence, my statement still stands. Boxcryptor is unfriendly, but hey, I am a big fan of EncFS, and really happy that Boxcryptor builds on top of EncFS. And my first post provides the workaround, so that Boxcryptor works with SkyDrive
There is no side effect either. Once SkyDrive links to the encrypted directory, it remembers the location and does not complain anymore. And when you restart boxcryptor next time, it "registers" itself to .bc extension once again.