I have done some tests with sharing the same folder on different clouds (One Cloud, Google, dropbox,...)lately.
To be honest, it seems to give nothing but problems. In fact, the files seem to be in 'sync mode' all the time and the services take a lot of memory resources. I think the reason is the following:
one cloud (f.ex. dropbox) sees a new file and starts synchronising. Once done, it seems that something on the folder or file is modified. The other cloud starts syncing as well. Once done, dropbox sees a change in the file and resyncs. But so does the other cloud when dropbox has synced.
So both clouds seem to be syncing all the time.
So I finally manned up and just went for it. As of April 2015, the OneDrive sync engine on Windows 8.1 is sophisticated enough to recognise the files, and avoid all of the issues I feared in the question. I clicked on the notification area icon, and clicked 'Resume synchronisation'. Whilst it started resuming, I copied the local files into the OneDrive folders, choosing to 'replace all' the not-downloaded OneDrive copies. After a moment, Windows realised they were the same files and didn't upload/duplicate them.
However, I did have some issues.
1) Because I had not synced OneDrive on that desktop for so long, when I clicked 'resume', it looked like nothing was happening. But rest assured that it is indeed syncing. There was no way to pause the sync whilst it was in the process of resuming.
2) I accidentally clicked 'make online only' on my OneDrive folder in the file explorer, whilst it was resuming syncing. Don't do this. This messed things up, causing some duplicates (with the name of the desktop computer suffixed to the filenames). Luckily, only a small proportion of files were duplicated. This resulted in, for example, a DSC_0001.jpg [the original, online-only, syncing] and a DSC_0001-brianPC.jpg [available offline, syncing]. If I tried to delete DSC_0001-brianPC.jpg and then re-replace DSC_0001.jpg with the local version, it had to re-upload DSC_0001.jpg unfortunately. So make sure not to click 'make online only'.
3) Before I started, I decided to run the OneDrive troubleshooter to reset OneDrive on that desktop. I thought OneDrive would start from square one again, on that desktop, but actually the OneDrive files and folders were unaffected. In fact, the sync resumed afterwards, earlier than I wanted. This didn't really matter in the end.
Extra
I suspect that one factor that can determine whether OneDrive will recognise (i.e. not duplicate) the files depends on the 'date modified' metadata. Wait, I don't think so actually. Perhaps it is more to do with which hard disk the files you are using to replace the OneDrive files are on. Or perhaps it just gets messed up if you accidentally make files online-only.
Best Answer
For future users: I solved my problem by mapping the drive using the instructions with pictures found here on laptopmag.com. In Case the site moves etc...
Please note: The alternative command line method described on superuser here using
net use
does not work for my problem as it caused the drive on my computer to map as a one drive folder which is no different that using the app.For some reason the Gui map as network drive created a mapped drive that I can copy the folder to the existing cloud folder. Robocopy automatically ignores identical files in source and target while changed local files replace the destination cloud files. With /mir option the files on the destination that aren't in the source are removed so for now I can get by with
robocopy .\src .\dest /mir
.Update: Using robocopy used to work or has worked before on onedrive mapped as a network drive, however as noted in the comments by some at the link I got permission errors in creating folders and files "ERROR 5 (0x00000005)" when using robocopy. As an aside syncback pro worked great as a temporary solution because it has a full featured 30 day trial and I only needed to do this once but it is a paid app which is not a valid answer to a question. There are always free solutions and alternatives, one that I haven't tried can be found here.