I have a huge project that contains several 3rd party classes and tools that are in latin1 charset, but the core and rest of my site is all in utf8. To avoid having transliteration prompts pop-up everytime I open one of the utf8 files (which is usually what I edit), I set the default encoding to utf-8 in the IDE Settings.

The problem with this is that if I want to do a project-wide search and replace, I am being prompted EVERYTIME the program encounters a latin1 file even if the string I'm searching for is not contained in the file.

This is EXTREMELY annoying because there's no way to cancel the search and I have to click "transliterate" on every single prompt (sometimes over 50 times...).

Is there a way to prevent transliteration prompts altogether when doing search & replace? (checkbox to search for textual string, disregarding charset) ?

It's not safe to edit or replace files opened in wrong encoding or you may get corrupted content. That's why this functionality was added.

If your project has different encodings in the files, you may want to set appropriate default encodings per directories. See Properties in the popup when right-clicked on the directories in the Workspace window.
Once encodings are set, you won't experience any problems with transliteration.

Ahhhhhh! That works then... I didn't see that option before... Thanks!

Unfortunatelly it is not possible (to my knowledge) to set the encoding for a whole project or for a workspace. Half of my projects are ISO-8859-1 based the other half are UTF-8 based. I can only set the encoding system-wide in Tools->Settings or based on directories within a project. The middle layer is sadly missing and I find myself clicking through the translit dialog very often...
Cheers, Jörg.

Fortunately it's possible. See properties for the project's root directory. Project Properties-> Properties (on the right, next to Root directory input)
The same way you can set default encoding for the files in subdirectories.

Whow, this is great news. Definitely makes my daily editing live much easier! Thanks for the hint, Dmitri.