The novel "Present Tense" was supposed to be a direct sequel to "The Naked Time". The premise of that book was that the Enterprise was heading to a remote part of space to lay low for the three day period in order to avoid meeting themselves.
Are you talking about the 3 part series, book one the janus gate?
I looked up the book and the summary doesn't really mention anything like " after being thrown back 3 days". I'm not saying your wrong because I have no clue. Just curious.