Yes, you can add, remove, or preserve captions as you transcode your video from one format to another.
Supported input formats:
Embedded: CEA-608, CEA-708 (MPEG-2 only) and mov-text
Sidecar captions: DFXP, EBU-TT, SCC, SMPT, SRT, TTML, WebVTT
Supported output formats:
Embedded captions: mov-text (MP4), and CEA-708 (MP4 and MPEG-TS)
Sidecar captions: DFXP, EBU-TT, SCC, SMPT, SRT, TTML, and WebVTT
CEA-708 captions are embedded in the H.264 SEI user data of the stream.