System.Threading.Tasks.TaskCanceledException: A task was canceled.

In general modifying the folder should not affect probability for exception appearing, but cannot prevent it. Some decrement may happen if different files/folders appear in different namespaces (namespaces are locked independently, so less likely compete), but better don't rely on.

Again, try to schedule the uploads in non overlap way and handle the possible exception in proper way. Example of such exception handling (again just example and far from optimal) follows:

private readonly int retryLimit = 20;

...

var backoff = 0;
var rand = new Random();
var commitInfo = new CommitInfo(filePath.Substring(filePath.LastIndexOf('/')),
    WriteMode.Overwrite.Instance, false);
for (var i = 0; i < retryLimit && !string.IsNullOrEmpty(sessionId); ++i)
{
    if (backoff != 0)
    {
        Console.WriteLine("Ограничение при завършване на файл {0}. Нов опит след {1} милисекунди...",
            commitInfo.Path, backoff);
        Thread.Sleep(backoff);
    }
    lastCursor = new UploadSessionCursor(sessionId, (ulong)fileStream.Length);
    memStream = new MemoryStream(buffer, 0, 0);
    try
    {
        await dbx.Files.UploadSessionFinishAsync(lastCursor, commitInfo, body: memStream);
        sessionId = string.Empty;
    }
    catch (RateLimitException rateLimit)
    {
        backoff = (int)(backoff * 1.1);
        backoff = Math.Max(backoff, rateLimit.RetryAfter * 1000);
        backoff = Math.Max(backoff, 1000);
        backoff += rand.Next(500);
    }
}
if (string.IsNullOrEmpty(sessionId))
{
    Console.WriteLine("Качването на {0} приключи \ud83d\ude09.", commitInfo.Path);
}
else
{
    Console.WriteLine("Неуспешно завършване на файл {0} след {1} опита \ud83d\ude15!",
        commitInfo.Path, retryLimit);
}

The above just shows how my advices (from previous page) can be implemented. Here sessionId represents a session ready for finishing (i.e. content uploaded already).