Are you parsing the string input from a file or the standard input of something?
scan(what='character',sep='\n')will read data from stdin()and automatically escape quotes. Same as from file
>scan(what="character",sep="\n",allowEscapes=T)
1: I'm watching "Prometheus"
2:
Read 1 item
[1] "I'm watching \"Prometheus\""
>
>scan(what="character",sep="\n",allowEscapes=T)
1: "I'm watching "Prometheus""
2:
Read 1 item
[1] "\"I'm watching \"Prometheus\"\""
Once you get your input, you can use regex to replace hidden inner quotes ... (I think! - it can be tricky reg exp)