Resources folder too big, files missing on build

So i have a proyect in which we animate lots of stuff frame by frame, and each frame is loaded from Resources. I recently added an XML file to adjust scene order loading, and whenever i try to load the xml file from resources it doesnt work, it returns null as if it wasnt there. This happens only on a build (im doing it for Windows x86_64 at the moment from Unity5). (Also some of the images on the initial scene are missing, as if they werent on resources either)

On the editor it works perfectly, and if i deleted lots of images from the resources folder, eventually it was able to read the xml file perfectly.

So my question is, how could i fix this? I know this way of handling animations is terrible, but since it was a quick project it was made this way.

Thanks, I appreciate it :)