Multiple projects can already be integrated with a good degree of seamlessness, as demonstrated in this post. And by design that is already the answer to your question of what to do if a project grows too large for your comfort zone (waiting for backups and so on). Maybe in the future we’ll make that a bit better (I can think of a few obvious improvements), but for the moment, I don’t really see how breaking large projects apart into smaller ones is any different than what you are proposing?
I do also agree that something seems a bit off with the technical problem you’re facing with sync. Unless you do just mean it takes a long time to upload the entire .zip at the end of the day, sure. But the project itself, if it is being synced, shouldn’t take more than a few seconds to close. Most of the changes you’d have made during the day would have been saved and synced a long time ago, seconds after you made them. What gets saved on close is a few housekeeping files, like the search index, some settings, the internal binder backups, and any trace content files that were modified seconds before closing.
Even the largest of those files, the search.index on average, is going to be a modest upload in the grand scheme of things.