I went through the HISTORY /R code line by line, and I'm 100% certain your problem isn't with HISTORY /R, which definitely does not do any parsing of the file, ever. (Except for the aforementioned check for an escape as the last character on a line).
HOWEVER ... if you have defined HistoryExclude, then before the line is added to the history, the first command is extracted so it can be compared to the HistoryExclude value. (This is true of every way you might add a line to the history, not just HISTORY /R.) If you have mismatched back quotes, they can trigger an error message then (though that won't prevent HISTORY from adding the line). I don't consider this a bug, because you'd get the same error message if you entered it on the command line.
There has to be more to this than you've told me so far ...