My roosters have suddenly gotten mean to the hens

sounds like your male to female ratio is too high.   for just three hens, i would think only one rooster would work or else they would be constantly trying to outdo each other and consequently abusing the girls.  since it hasn't happened until today, maybe it's some other dynamic.  i'm very new to the chicken world.  mine aren't even grown yet.

good luck getting things smoothed out again.

With only three hens, two roos is way too many. You're lucky it's been okay until now, but you need to ditch one rooster and see how things go. I've also had a rooster stalk a specific hen, when they were free ranged and he had 20 other hens to chose from. I'd pull them both out, let the hens heal and regroup, then put your favorite rooster back in and monitor. If he's too hard on the hens by himself, pull him and try your alternate. You might just need to keep them both out until your littles are old enough to take some of their attentions. As stated, your first responsibility is to your working hens, they're the ones that make your product.

I agree that you need to remove one of the roosters.  Generally you should have one rooster for every 10 to 12 hens; as a minimum.  I had two roosters with almost 30 hens and still had issues between the boys.  They are being boys!

As far as separating your shy girl... probably not a good idea as she'll have to come in as the bottom hen when you put her back in with the rest.  She'll be a target again.  You need far more hens or no roosters or only one rooster.

One thing I have done - I have one adorable little silky hen and the rest of my 30 some chickens are twice her size.  (Except my silky roo)  At night we lock her up on a protected side of the coop.  She is with the other birds but has chicken wire between them and her.  During the day she is let out with everybody in the run or to free range.  Since there is no place for her to get protection from the bullies of my bunch, this is the best way to protect her when there is no where for her to run to get away from being chased.

It's interesting that even my two boys had their favorite girls - those poor girls had no back feathers and did, at times, have blood.  I ended up re-homing my most aggressive rooster as he was just too hard on my girls. 

Finally, there are never any silly questions... always ask.  You are learning and wanting to take care of your flock the best way you can.   We all started as complete newbies at some point in our lives.

I'd say to separate the ROOS from the hens. And immediately. Keep all of the hens together.   If you want both roos, would advise to keep them in the other dog run for majority of the time and only allowed occasional short visits to the hens.

The roos are being too aggressive. If you still want one and part with another,  watch their "supervised visits" one roo at a time and see which one is being more of a gentleman to the hens. 

But seriously, confine both roos to the dog run ASAP and keep them there until the hens have recovered well.   They don't really need a roo to be with them anyways.

I had to re-home one of my roosters recently - for the same reason.  I knew I only needed the one roo - so I picked my favorite and sold the other one.  I usually can find buyers for my extra roos pretty quickly via Craigslist.

I wouldn't tolerate a rooster that wasn't a gentleman to the hens.   Getting rid of my first rooster broke my heart too (he was so pretty), but I'm sure he won't be the last.