I don't know the technicalities of this, but I do have the situation where I and my assistant operate a common dropbox with two different computers going on and off at different times.
The answer to your question is that when you connect with the Cloud, Dropbox knows (somehow) that the version currently on the Cloud was originally synced from your computer. So if your computer version is different, that is the version that will be synced to the Cloud.
If two computers (say A and B) are using the same dropbox, and each make changes offline, then the first computer powers up (let's say it is computer A) will generate a sync of its update to the cloud. So now there will be same version (containing the A update) on A and Cloud.
When computer B is powered up, Dropbox will realise that computer B's version of the file is not only different from the current cloud version (which is normal) but different from the last time Dropbox synced from it. So if it were to sync B's file to the A version, B's changes would be lost. So what Dropbox does is make a copy of the B version and add "B's conflicted file" to the file name. B's original file is then synced to the A updates. The conflicted file, containing the B updates, is then synced to the cloud and back down to A.
Deletions, and conflicts arising from selective sync, are handled in a similar way
A conflict also arises if one of the computers does not close the file before powering down. Syncing does not occur on an open file, so in this case B's updates will be the ones that are synced, and A's open file will end up as a conflict. This can be a huge pain to harmonize, but this is our fault, not Dropbox's.
Hope this helps.
TL,DR: You don't have to worry about any of those points.
The encryption is on a layer bellow the files, so from your games' point of view, nothing changed. It's almost like cloning your Samsung HDD to a Hitachi one, with exactly the same size, and putting it back.
Your games will still run with almost the same performance. You will incur on a very small increment on load times, because the back-end will have to decrypt the data before your game reads it, but the penalty will be almost negligible. Unless you have a program to measure the timings a couple of times, you will not notice it.
The same applies to your Dropbox files: they don't change. Only the low level representation of the file will be changed, but for your applications, they are still the same.
So encrypt your disk. Your files will be there, untouched, but remember the password. If you forget the password, your data is lost.
Best Answer
How cloud synching works
OneDrive support replied & told me they don't support encrypted files (i.e. they use date & file name to detect changes, not file contents \ hash).
I've logged a request for them to use hashing: https://onedrive.uservoice.com/forums/262982-onedrive/suggestions/13292115-detect-changes-to-files-based-on-the-file-contents
I haven't found any information yet on how Dropbox \ Google Drive detects changes.
General solution that is tedious
The only general solution is to:
OneDrive then detects it as a new file and uploads it (and deletes the old one in the cloud)
Best solution (if you use Veracrypt)
However here is the ideal solution if you're using Veracrypt (Truecrypt):
Now the file date changes every time you change the contents and cloud backup services will always reupload it.