Convert Quicktime movie(mov) to MKV

i started doing video editing in final cut x , export format .mov.
handbrake doesn't handle .mov files , can't find alternative convert them .mkv. i'm prepared pay little money, can't find program trust. recommendations?

 

handbrake can handle .mov files, though has problems prores codec.
have tried makemkv yet?

, why need .mkv?

 

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