Skydrive (and many other similar services, including Google Drive) do not have the ability to do blockwise synchronization -- their smallest units are files. You are, unfortunately, out of luck if you are tied to both SkyDrive and TrueCrypt.
A workaround may be to switch from TruCrypt to encfs when using SkyDrive -- instead of encrypting an entire partition/imagefile like TrueCrypt, encfs works on files and directories (but still provides access via a separate drive letter on Windows or a separate mountpoint in *ix). The encryption is sound, but naturally you are making a tradeoff -- while Skydrive will not be able to discern the contents of your files (or their filenames), the way encfs works necessarily leaks information about the size of your files (and the approximate length of your filenames).
I have been using http://members.ferrara.linux.it/freddy77/encfs.html on Windows with Google Drive for a while without issue. While you still don't get intrafile-syncing, if the actual files you currently keep within your TrueCrypt-volume are small(ish), only the ones you actually change will be synced.
Before reinstalling them, create links using mklink, such that they appear to be in the right place.
The default locations will be automatically populated with your files after installation, and there should be no redundant uploading either.
Example, as requested:
Let's assume we're dealing with DropBox. This will apply to the others too, but for convenience I'll explain just the one.
- Stop DropBox from running (I think it is a Windows Service)
- Move the data from
C:\Users\Fortune\DropBox to D:\Cloud\DropBox. Don't copy, because the folder on the C: drive must no longer exist for the next step to work correctly.
- Create a directory junction* with
MKLINK /J C:\Users\Fortune\DropBox D:\Cloud\DropBox
- Check in Windows Explorer that the junction is there. It should behave like the real thing.
- Start DropBox again.
What happens is you fool your OS into thinking that the folder on the D: drive is where it always was.
When you then format the C: drive, the junction point goes away, your data is safe, and when you install DropBox again, you just recreate the junction point before installing it, to make sure it uses the existing data. No duplication or re-uploading required.
**(I've typed this edit on an iPad with no access to Windows, so I hope the MKLINK syntax is correct.)*
Best Answer
It is possible to change the Dropbox directory under its advanced settings. You could set it to the SkyDrive folder. You can not change the SkyDrive folder in its settings. Most likely due to its integration with your Windows account.
I dont see doing this will cause a problem. Definitely backup your data and test this before committing any important data.
EDIT: I just tried this, DropBox will create a DropBox folder in the SkyDrive folder. If you can live with that, then this will work. So just save everything in the dropbox folder (under skydrive) and everything will be synced between the two accounts.