Deletion of file during upgrade is not working properly.Answered

I am facing one problem with the a particular file (dll) being deleted in the newer version. I have deleted that file from the newer version (intended) and on newer version upgrade, that file gets deleted from installation folder also. So perfectly fine so far. But when I close and reopen our software, repair dialog appears and that restores that deleted file. How can i get rid of this repair dialog as I do not want that file to be restored as that is causing conflict and not allowing application to run properly. Our application is running on Windows 10 and we are using licensed version of wyBuild 2.6.18.4. Please let me know if any further detail is also required.