http://www.inkjetmall.com/tech/showthread.php?1023-The-lessons-I-ve-learnt-from-using-desktop-refillables-over-9-years
A couple of observations.
Head strikes are to be avoided at all costs, not least because they will ruin the print and spread ink around under the print head, bringing closer the day when you'll need to clean under the head. I don't recall reading of a damaged print head from a strike, nor had it happen, but I imagine that it's possible. I think you'd have to be unlucky, but that kind of bad luck would be expensive.
Easy does it is good general advice. There are delicate parts involved. IJM recommend performing the routine in their video on a regular basis as preventative maintenance, especially the capping station and wiper blade. I'm not inclined to do it as often as they recommend, but given that there will be a head clean at each refill, then if you have the time it's a good time to do it. I only clean under the head when it's needed, or if there's been a head strike or leaking cart.
Ditto for using the IJM cleaning kit to push flush through the head. I wouldn't have called it "really aggressive", but you do have to be gentle, especially if you have a stubborn clog. There are people who have ruined a print head (expensive) by forcing too hard and rupturing the membrane between channels, but having done this a number of times, I honestly think you'd have to be really ham-fisted to have it happen, and the clog that caused it may have meant that the head couldn't be retrieved anyway. One trick I read is not to push the tiny syringe all the way to the bottom, as this risks pushing air into the head, which would complicate the restart. Better to leave some ink in the syringe, as this should mean that the head is full of liquid.
I strongly endorse don't rely on head cleanings and patience is a virtue. Not all gaps in nozzle checks are genuine clogs. With refillable carts they're often air in the system or flow issues, and head cleans can sometimes make matters worse, as well as consume ink from all channels. Purge patterns are a better starting point and I only resort to a head clean if absolutely necessary.
It is possible to use QTR to run a purge pattern on just the channels with the missing nozzles.
http://www.inkjetmall.com/tech/content.php?166-Flush-individual-channel-using-QTR-Calibration-Mode
This article says not to use this procedure to unclog a printer. But you won't know whether it is a genuine clog that needs heavier treatment, rather than air in the system, until you've tried it. Someone from IJM claimed that you could burn out a nozzle doing this, but honestly, I printed a LOT of purge patterns with nozzle gaps and my heads are all just fine, thanks. (It's also possible to selectively purge channels using QTR custom curves, but I think most people will find the IJM approach the simplest.)