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handbrake should suport ass what you talking he even [Censored] convert srt to ass i just post about this for having a passtrought option and keep sub in original format.
SSA/ASS is supported by handbrake, but it must be muxed into the source MKV file. Unlike SRT subtitles, SSA can (and usually does!) support fonts and such that must be included with the subtitles.
You can use mkvmerge to insert the SSA/ASS file and its associated fonts into the source, and run it through handbrake.
kilerport - I would recommend very good program called the Subtitle Edit (freeware). Just open the the mkv video file containing the ass subtitle in it. The content of the ass file appears in the window and then you can edit it or just save it as the .srt. Then using the mkvmerge you can add it to your mkv... You can even unclick the unwanted ass file in the mkvmerge so it would not appear in the new mkv file created by the mkvmerge.