I have a team where I have 12 players injured going into next week, I'm playing a couple of the less injured ones but still only have 43 active players.
If I activate 2 or 3 of more injured ones to get me up to 45/46 active players but remove them from the depth chart will they actually be used or does not being in the depth chart take them out of the rotation completely thereby meaning they can't get re-injured ?

Depends on how deep your depth chart is at those player's positions and how low or high you set the fatigue levels. As the AI substitutes in fresh players, ... if it gets to the bottom of the depth chart, then it will pick the next most qualified player that isn't more fatigued than the level you have set. Unfortunately, this is most likely to happen during the 4th quarter.

Set your fatigue levels to keep players in those positions a little longer, and assign a few extras at the bottom of your chart.

Of course, if you set the fatigue numbers too high, You'll wind up with some fresh injuries ...

I'm lacking a way to get players like this https://ags.myfootballnow.com/player/250 into IR. Can't be right I have to carry someone I can't play for the rest of the season, just because his season-ending injury isn't deemed serious.

Going into the wild card week (week 16 just done a few hours ago), I have 5 players who will be out 3 weeks or longer. Something like a "If injury is more than 40% of the remaining season, they can be put on IR" would be helpful.

At one point, I had 8 guys who were at the top of the depth chart out with injuries of 3 weeks or more. At those points, I really miss those injury designations where you can pretty much take them out for like 8-10 weeks and then reinstate them. And season ending should be season ending, counting as season ends week 16. In PO's any injury longer than 3 weeks should count as season ending, so it's up to the owner if he wants to find short term replacements or just roll with it.

God knows, it's not like there's a bunch of super solid players on the FA list - but players who are able to run, at least.

Thanks Tarquin - I've already tried to fill out the depth chart at a couple of positions but hadn't though about raising the fatigue levels a bit,

Edit; Just realised it's a roster only league so I can't change the fatigue levels...oh well