My paper was withdrawn from predatory journal after publication, what should I do?
The most important thing you need to do is figure out the copyright status. If you have given them exclusive rights to reproduce the work, then you may not be able to publish it anywhere else. It is likely that the copyright transfer was part of a publication contract where the publisher has agreed to publish your work in exchange for the copyright transfer. Hopefully, the publisher will given up the rights you transferred to them. If they won't, you may need to get a lawyer to explore your options.

Having listed the paper in a scholarship application is problematic. Paper-based journals and journals that generate DOIs create a permanent record of the published papers. In your case, it seems a published paper has simply disappeared. I would write to the places you have submitted an application and explain the situation. something along the lines of


  The paper XXX, which I listed on my application, was published by YYY. Unfortunately, YYY is a known predatory publisher and has since made the paper unavailable. I still stand behind the research; attached is a copy of that work. I am currently working towards resubmitting the manuscript to a reputable publisher. I am sorry for any problems this causes.