What tool to compress

[toiday]

I'm using Handbrake to compress mkv files from MakeMKV. However, Handbrake can't handle subtitles. Is there any other tools to do the compression and retain all the subtitles?

[Woodstock]

News to me - handbrake handles subtitles just fine, as my 16TB of handbrake-compressed anime attests. If you have specific issues, provide them with a log of an encode that didn't work, and they'll help you find the problem.

Other tools depend upon your operating system.

[T'hain Esh Kelch]

You can convert the MKV subtitles to SRT, which works in Handbrake, using Subler.

[Woodstock]

I think Subler is Mac only, though.

Most subtitle types that work in MKV files should be usable in handbrake, though. SRT is the only one you can "add in" as a separate file, though; Substation Alpha (SSA or ASS) subtitles have to be merged into the MKV file first, along with any special fonts required.