The midfielder’s name was nowhere to be seen on the team sheet for the goalless draw against Mark Kennedy’s Imps.
That’s despite the 29-year-old coming on as a second-half substitute in last weekend’s thrilling 3-3 draw at Sheffield Wednesday.
But according to Cowley, Tunnicliffe’s one-minute cameo against the Owls triggered a hamstring complaint which prevented him from training all week.
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He was, therefore, not available for the Imps game, which saw many members of the Blues squad take the field despite a sickness bug running through the squad.
Prior to the game, Pompey fans were introduced to new midfield signing Tom Lowery, who has joined following the expiry of his Crewe contract at the end of last season.
His signing on a free transfer on Friday night means the Blues now have six midfielders vying for two central-midfield spots.
When asked BBC Radio Solent about midfield departures, he said: ‘Potentially.
‘I think you never quite know how a transfer window is going to unfold, but I’ve been in football long enough to expect the unexpected.’
Louis Thompson and Marlon Pack were the two midfielders Cowley opted for for the visit of Lincoln.
Like Tunnicliffe, Joe Morrell missed out on the game through injury, while Jay Mingi was introduced to the action in the second half, coming on after 70 minutes for Thompson.