The Northern Irishmen, who were partnered in the Seve Trophy and World Cup in 2009 and 2011, have played together six times in the Ryder Cup.
Reports have claimed that the relationship between the pair became strained throughout McIlroy's ongoing court battle against his former management company Horizon Sports Management, who also represent McDowell.
However, McGinley said in a press conference yesterday that he is considering splitting the two competitors for "tactical" reasons.
"Both of them have assured me all along that there's no issues and that's the way I've always seen it," McGinley told reporters. "Whether they come together or not is another story.
"Three or four months ago, I had a very strong view that they would have been, but the more I look at their statistics and the more I look at the different value I have with them, I'm thinking there may be value in not doing it. If I don't decide to play them, it would be for tactical reasons."
The competition gets underway in Scotland on Friday.