Website script converts videos to flash and plays online using Ultimate Media player I lost all my flash formated files but have the wmv files

I have a website that uses a script called social media v2.2 sold by a company called mediascripts.com when I upload a video the script converts it into flash format using ffmpeg when I moved my server I lost all my flash encoded video files but still have the original .wmv files . Everyone I talk to tells me flash is done and everything is mp4 or this HTML 5 can someone give me some reassurance on the future of flash . ANd is there a way to get a flash player that supports both the flash files and the mp4? Also is there a tool a can put on my server which is a Linux Apache 2.2.29 that will automatically in the background convert all my wmv files into flash and Mp4 ? What is the best suggested solution for my issue.