The defender avoided being cup-tied after missing the comprehensive 5-0 win over Auchinleck Talbot which laid Hearts’ ghosts of Brora Rangers to rest.
Souttar watched from home nursing an Achilles injury and Neilson insisted there was nothing more to it, other than the player's welfare, despite a bid to expedite his summer transfer being received – and rejected.
Neilson expects him to be available for Wednesday’s cinch Premiership clash with Celtic and explained: "John had a problem with his ankle after the game the other night. I know everybody thinks it is to do with what is happening, but it was on his Achilles and we felt there was no point in bringing him down here.”
He added: "We’ve had a bid in, which has been knocked out the ballpark, so we will wait and see if anything else comes in.
“He will be in the squad for Wednesday until something changes."
Though they began their Scottish Cup campaign without the Scotland international, Neilson says he intends to keep and use his centre-half to maximise his side’s chances of European football and Scottish Cup glory.
The Jambos last lifted the trophy ten years ago with a 5-1 win over Hibs at Hampden, rounding off a campaign that began with eliminating Talbot.
While hoping for the same outcome, he insists he will need all his best players to do so – including Souttar.
"We value John very highly and if anyone is going to take him in this window, they’ll need to pay for him because we are aiming for the Scottish Cup and European football and we need to keep our best players.”
Without Souttar Hearts still named a strong line-up with Craig Halkett and Stephen Kingsley marshalling the defence to progress without the issues experienced in Brora a year ago.
"Last season was a tough one to take and we knew coming to this we had a bit of making up to do. Hopefully we have done a wee bit but we want to go all the way.,” added Neilson.
"Tommy Sloan has been here 17 years and built one of the best junior teams for a long time. For us to come down and win the way we did, I’m pleased.”