Wondershare UniConverter is very reliable,fast (uses GPU´s Encoding Abilities too if supported) and stable (Windows 10 x86).
If your CPU/GPU is powerful enough you can convert up to +10 Videos at the same Time.
Those are really just container formats. The codecs are the important part (you can check the codecs of video files with either MediaInfo or open them in VLC Media Player and press Ctrl+J). Luckily, there's an easy way to change the container format with ffmpeg without re-encoding them and losing quality.
Here's the command for a single file. This will create a new file and leave the original untouched:
ffmpeg -i video.flv -codec copy video.mp4
I'm sure there's some way to do a whole folder at once but I usually just make a batch file with the ones I want to convert.
Another free Windows option is Format Factory and it can do batches, but be real and use handbrake. I have a pi 3 that runs handbrake all day long and converts videos in placebo quality, takes forever but files are small and run fine from my pi4 Plex server. Oh some one mentioned VLC? She has a built-in converter too, Google it.
It's Just That I Have Been Having a Hard Time Ever Since That I Saw Awful Hate Images of Ami Onuki, Sky (Friday Night Funkin'), Rabbids and Teen Titans Go. I Just Wish that People Would Change and Start Making Fan Art of Ami Onuki, Sky, Rabbids and Teen Titans Go Instead of Just Making Hate Art out of Them for a Change.