Head coach Clarke left six players behind in Spain as a precaution as Scotland drew with Holland in their first warm-up in Portugal last Wednesday, while Fleck had an even longer stay.
But the Sheffield United midfielder's positive test proved an isolated case and the 26 Scotland players all came through Covid checks after reporting to their Rockcliffe Hall base near Darlington on Wednesday night.
Striker Kevin Nisbet said: "The camp's in a very good place now. We had two days back home, we came in and got tested right away and sent to our rooms. Thankfully everyone came back negative.
"With the magnitude of the tournament coming up, everyone wanted to be negative and not have that holding them back. We are delighted that everyone is negative and now we really start to go and put a marker on the tournament.
"It's great that Flecky is back. He obviously had a tough time testing positive and he has just been in his room ever since. So he got a wee round of applause this morning from the boys.
"He wanted to come in and start well and be in contention for a place and it was tough for him to test positive for Covid but he's a strong character and he'll bounce back. He was good today in training."
The ever-present coronavirus threat will ensure that the Scotland squad's activities at the luxury hotel next to Middlesbrough's training ground are rigidly monitored.
"It's hard because there are Covid rules and you still have to sit two metres apart," Nisbet said.
"Apart from training you have to relax because there are tough games coming up and a lot of tough training so, every opportunity you get, you have to relax and rest and recover.
"The place is massive so you can go out walks and there's facilities and the training pitch is great, we have a spa we can use.
"There's a golf course here but I'm not very good. I will try. I think Robbo (Andy Robertson) fancies himself and Greg (Taylor) as well. There's a few decent players, John McGinn is decent as well.
"There's a few good golfers so we just need to tag along with them."