I think that’s fine. The config is in a different file so it will just be like an initial backup. If you think there’s a chance that initial backup won’t complete without interruption, you could do a small starter backup to get something uploaded, add folders slowly (gets more intermediate points in case issue arises), and so on. Easiest is to just do it, but interrupted initial backups don’t recover well (so might have to be done again).
Failed first upload has more discussion for a recent case.