I am really enjoying Textastic (for iPad), but I too have stepped into the mess that can be after having modified files in the app and on a dropbox account.
Instead of using timestamps to compare files and keep track of where they came from, I would suggest to have a natural date display on files (e.g. today, yesterday, then 20XX-XX-XX) to quickly see when files were modified in app and on remote system.
Another feature on top of this would be the ability to display a list of recently modified files (I now use the accessed files list, but not all I have changed)
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