Hylton was taken off at half-time in the 3-2 win over Shrewsbury Town, whilst Sheehan missed out on being involved in that squad entirely.
The next few weeks could also see the return of Luke Berry to matchday squads for league games, but Jones is happy for the midfielder to take as long as he needs to complete his recovery.
The gaffer said: "Danny has recovered well. It's just a minor thing anyway in terms of his hamstring, which was a little bit of leftover from what it was last year, but it's nothing to worry about.
"We're in good shape in terms of the squad. Luke Berry is probably a week away, it may be too early to include him, I don't know, but he has trained well again today, so the squad is in good shape.
"Alan had two injections on Friday into his heel. That inflammation seems to have gone, it doesn't seem to be a problem. We gambled a bit in terms of getting it done on a Friday before a game and the gamble paid off, so he should be pain free."
The Welshman has used both Marek Stech and James Shea so far in league games, with the manager wanting to try and establish a regular first choice keeper, but he expects it to be a real challenge between the two to try and nail down the position.
"I don't want it to keep changing, but it will be a battle," he explained. "I want them to keep pushing each other. Last year we had Marek playing a majority of the season, but James kept himself in wonderful form and a frame of mind so when he was called upon, we finished the season very strongly and that was a credit to him.
"That is the competition I want. It's a different situation to a couple of years ago when we were taking loans, so I don't want it to be chopping and changing, because changing your keeper is a big thing because of the understanding and so on. I want them to be battling it out, I want them in good form and I want them pushing each other."
Going up a division has seen the Town face a number of tricky tasks already in the teams they have faced, with Jones saying that he, like his players, is on a learning curve all the time as they get used to third tier football.
He continued: "It's testing. In my first year here, from knowing everything about the Championship, then going to League Two, and I had to learn. Obviously I have been preparing for League One for a long time. Last year we had a lot of things our own way, but I had been here a year-and-a-half before that. I had to learn quickly then.
"I remember going to Wimbledon and controlling the game I thought, and then losing the game from four goals in quick succession. Those are the things that can happen. So I learned about the league a lot and then I had to do that the following year, when heartbreak struck in terms of the play-offs, so I am on a constant learning curve.
"I will have to be tactically good and strong and my players will need to be. But we're equipped for the level. We've got no problem with the level as you can see in the games that we've played. Apart from a 25-minute period where we were defensively so, so naïve, I think we've been in decent form."