One of two things is going on:
1. Severe tendonitis which hurts but is treatable without surgery.
2. Rotator cuff or shoulder labrum tear - This is what you don't want because it requires shoulder surgery.
If it took about three weeks of HS practice for the pain/soreness to return, then that is a good sign because it usually means tendonitis. If her shoulder hurt immediately after taking 10 days off, then I would have bet on a shoulder tear.
But, again, go get an MRI just to make sure there is not shoulder tears and damage. If the MRI shows a tear, then she will need surgery and you want to get this done ASAP. Depending on the particulars (labrum capsule or rotator cuff muscles), the recovery time can be anywhere from 3 months to 12 months (just think about how ESPN says a pro pitcher is out for a year because of surgery). You will also need to communicate this fact to the collegiate coach ASAP - The majority of coaches will be disappointed but know it happens, and would redshirt her to make sure she recovers - we all learn not to rush shoulder recoveries. If the coach reacts negatively, then you want to know this now, so you can make adjustments/revamp the recruiting effort instead of being 'surprised' come November.
If it is just tendonitis, then she will need to start a comprehensive shoulder rehabilitative and strengthening routine. Initially it means rest, ice, ultrasound stim and anti-inflammatories (like Aleve, which was the prescription anti inflammatory drug when I played). After her soreness moderates, then she will engage upon a shoulders strengthening plan which all baseball pitchers do no matter what. The reality is that she has swung so much, her shoulder muscle cage has weakened, and this weakness results in tendonitis. By engaging in a rotator cuff and shoulder strengthening plan, her shoulder joint will stabilize and get back to being strong enough to handle the swings.
She must strengthen it because what she will be doing in college is much more intense than what she did in club - Hard to fathom but true.
1. Yes, you should be concerned about her shoulder affecting the NLI. As I pointed out, hopefully her collegiate coach is old school, but many AD's have become so focused on money that they will not provide medical support if there is any documentation of shoulder issues and the Training room mandates you send in all medical histories. So, even if she signs her NLI and then the shoulder pain hits again after the 1st week of the season, you could really be in a bad spot because the school would have no issues cutting her.
2. My daughter would immediately stop swinging, go get an MRI and we would proceed as MRI dictated; either surgery or intense rehab routine - and HS Volleyball would be very, very low on the priority list.
Good luck and take the lead in managing this situation.