The installer damaged the yellow jacket on my gastite(CSST) line by chaffing it through a few holes during installation. Is there a method of repairing the jacket or is the line done(the actual metal tube inside is fine).
As long as it is inside, it's fine. The jacket is there to protect it during installation (such as what happens when you feed it through a hole) and to identify it as being part of a gas piping system. It also acts as thermal protection, but I wouldn't worry about a few nicks in the coating, it happens frequently when being shipped and installed. Outside, it also acts as protection against UV rays, so any damage should be fixed, such as with UV rated tape. Also, the pipe's integrity remains as long as any dents or crushing are less than 1/3 the pipes diameter.
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I also contacted Gastite who confirmed exactly what you said. They recommend using self-bonding silicone tape for jacket damage repairs when the Gastite is exposed to the outside or abrasive chemicals.