It's been several years since I messed with Wine, but it didn't take long then for me to decide that it was just more damn trouble than it's worth. I haven't seen much lately to convince me that this is no longer true. I decided that if I want to run Windows software, it's easier, and worth the cost of the license, to run it in Windows. This could be either a hardware install or a virtual machine.
Regarding the broken links. I seriously doubt that Linux "replaced your files with broken links". Most likely the links were there all along, and something happened to the files that the links were pointing to.