Bugfix and converting files

I have a modified ClipShare website and when i upload a video it gets converted to FLV then the script convert it again to MP4 so it can be played on mobiles. i have deleted the MP4 file by mistake but still have the original FLV files on the server. What i need? 1- Convert the videos i have from FLV to MP4. 2- Find a way to delete the FLV files automatically or just convert the videos to MP4 when uploaded so we can end this once and for all. 3- i keep on getting error emails i don't know whats wrong with this subject "Warning: message 1W8dx7-0004ZV-Gw delayed 24 hours" i need you to fix this issue. That's all for now, kthx.