Problem with CPU at 100% and RAM does not stop increasing

[Efficient_Good_5784]

I can't do that because it's a lot of content and it would take a lot of time,

A journey of 10 thousand steps begins with a single step.

...but everything is in mkv which allows it to be played on all devices.

Having MKV containers doesn't mean that it can be directly played on every client.

@TheDreadPirate already responded with the codec that are most likely compatible with a wide verity of clients and hardware:

H264 main video
AAC stereo audio
SRT or burned in subtitles
MP4 container

Note that Dread is recommending to use MP4 containers. MKV containers are more versatile, but have less compatibility with clients.

You need to verify what codecs the videos and audio are encoded in inside your MKV containers as well.
H265 video will be less portable across clients than H264.
FLAC audio will also be less likely to play well on most clients as compared to AAC audio.

Can't you cancel the transcoding of everything even if that means some content can't be played?

Yes, this is a per-user setting. You need to go into the dashboard and into each user's profile settings to disable the appropriate settings for them there.
   
The option "Allow video playback that requires conversion without re-encoding" is the option that enables remuxing to happen.
Just uncheck all three options (the two for transcoding, and the one for remuxing).

Doing so will result in your users getting denied when attempting to play a video that's not supported on their client.