Disable "Auto remove aux files" dialog in TeXworks

^{From my comment to a proper answer. :)}

The root of all evil relies on a hook named logParser.js inside <USERHOME>/.TeXworks/scripts/Hooks. If you are not sure where to find this path, TeXworks has a shortcut for it:

Namely, Scripts ▶ Scripting TeXworks ▶ Show Scripts Folder. Then you can access a folder named Hooks in there. Pretty easy, isn't it? :)

The file to blame is logParser.js,

which is a JavaScript code. We have two ways of dealing with it. Either by disabling the whole execution of this log parser via:

(Scripts ▶ Scripting TeXworks ▶ Manage Scripts)

And then unchecking the item Errors, warnings, badboxes under the Hook Scripts tab.

Or we can edit logParser.js directly. The function that deals with warning about auxiliary files is around line 373:

LogParser.prototype.WarnAuxFiles = function()
{
  for (var i = this.Results.length-1; i >= 0; i--) {
    if (this.Results[i].Description.indexOf("File ended while scanning use of") > -1) {
      if (TW.question(null, "", "While typesetting, a corrupt .aux " +
        "file from a previous run was detected. You should remove " +
        "it and rerun the typesetting process. Do you want to display" +
        "the \"Remove Aux Files...\" dialog now?", 0x14000) == 0x4000)
        TW.target.removeAuxFiles();
      break;
    }
  }
}

Although I could add a return statement right after the function body opening block, I'd favour commenting the offending parts. :) So:

LogParser.prototype.WarnAuxFiles = function()
{
/*
No more! (Dr. Who, The Day Of The Doctor)

                        _.._
                       /   a\__,
                       \  -.___/
                        \  \
                   (\____)  \
               |\_(         ))
          _____|   (_        /________
               _\____(______/__
                    ______

  ooh a duck! :)

  for (var i = this.Results.length-1; i >= 0; i--) {
    if (this.Results[i].Description.indexOf("File ended while scanning use of") > -1) {
      if (TW.question(null, "", "While typesetting, a corrupt .aux " +
        "file from a previous run was detected. You should remove " +
        "it and rerun the typesetting process. Do you want to display" +
        "the \"Remove Aux Files...\" dialog now?", 0x14000) == 0x4000)
        TW.target.removeAuxFiles();
      break;
    }
  }
*/
}

And we are done. :)