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May I ask, why is uploading via ftp not an option? Your edits would be easier, you could update your .muse in a monthly rhythm or so.
As long as everything works, I could not detect an issue. But maybe you use your muse and transfer it to something like this:
http://www.conmunicator.de/ This allows the complete muse to be transferred as it is to a maybe more stable CMS.
One advantage could be as well to add different admin levels. So you could provide different people to edit, what you allow them to edit.
At the moment I am in search about deeper questions like: Is there a way to update the .muse, once there are many edits done in the CMS of Contao.
There are possibilities to convert respectively build the site as a WP. I read too many hacker attacks to WP.
I am in support of what Uwe said.
IF you export your site via FTP then you do get an option of uploading modified files and edits only.
However, exporting to HTML does not give this functionality and resulting very long upload time.
And your site is really very big and well structured, so I understand you won't even like to any risk like dividing the site.
My latest update dealt with the master page footer so pretty much all of the pages reflected a change. I may need to do more research on some of Uwe's suggestions. Do you often come across users of Muse managing sites this large?
Personally, I haven't seen any user with a large and complex website created using Muse on this forum. But that is just my personal observation.