When moving multiple files into a location where copies may already exist, a confirmation dialog box is displayed. However, one dialog box is displayed for each file to be overwritten and all dialog boxes appear simultaneously, stacked on top of one another. Therefore, pressing the "Replace all" button is no different than pressing "Replace" -- except, of course, for the resultant confusion of the user. This appears to be a consequence of the decision to display one dialog box for each file rather than the implementation of the "Replace all" button itself.
I cannot reproduce this bug in thunar 1.6.3 ... "replace all" just replaces all files for me. You are sure that it is an issue of v1.6.3 ? Is it still an issue for you ?
Since there is no further information, I will close the bug for now. Please feel free to reopen if it is still an issue !