Harper has featured only once in the Rovers squad since the 1-1 draw at Crawley on February 18, when the League One leaders were beaten 3-0 at MK Dons at the beginning of this month.
With the loan window set to close on Thursday for the final time this season, the former Reading midfielder has been linked with a move away from the Keepmoat Stadium.
However, Flynn has denied that Harper, 32, is poised to leave the south Yorkshire club.
"It's something that's come from Twitter, like so many things nowadays," Flynn told reporters on Saturday following Doncaster's 3-2 victory over neighbours Scunthorpe.
"I've not spoken to James about it and I don't think he'll be going anywhere."