Your comments

While I could reproduce the problem with SVG files, the preview of the XHTML files I tried worked flawlessly. (I just tried this again)

Can you please send me an XHTML file that doesn't work for you to support*at*textasticapp.com or tell me a URL?
No problem. I'm glad it's working now :)
I just had a look at the source code, and the file changes are saved before the action sheet is displayed. You got me worried for a second :)

I don't know what happened there. If there were connection issues, you would have gotten an error message (if you didn't press the cancel button in the file transfer screen).

I just tried to reproduce the issue by adding a character to a file and immediately uploading it to my Dropbox, but it always worked...
I could add a third button to the alert: "Don't ask again" which would disable this message if you do a quick upload in the future.
That sounds like a really nice idea. Do you have any specific gestures in mind for some of those actions? (maybe two finger up for page up or something like that)
Did you try the builtin WebDAV server? This is essentially an HTTP server that can serve normal html and css files as well as images but has WebDAV extensions that make it possible to transfer files.

Have a look at the manual to see how you can start the server: http://www.textasticapp.com/manual/lessons/Starting_the_WebDAV-Server.html
How exactly would you like to see this implemented? Should Textastic ask for a password when tapping on the "globe" button before it shows the remote connections screen?
Thanks, customization of the additional keyboard row is planned for an update: http://feedback.textasticapp.com/feedback/7441-more-key-sets-configure-additional-keys/
I thought a lot about this when implementing the quick upload feature.

In my opionion the override alert should stay:
The uploading option only appears if you are working with a file downloaded from a FTP or Dropbox server. If you didn't, the first option will be to mail the file.

So, if you accidentally tapped on the upload action, this is your last change to prevent overwriting a remote file. This can be a destructive process on a live web server, so Textastic warns the user.