Eagle20 works (without a doubt). It doesn't kill the PM that is hanging around, it prevents it from finding a new place to hang around, and protects the still uninfected areas of the plant (and becomes systemic for a long period of time in the plant, which prevents it from returning for a good length of time). However, it is really nasty stuff. Cover your skin (completely - mask over your face - cover your hair), use a real respirator (not a fucking cloth dust mask from Home Depot), suite up (use a plastic painters suite, not a CLOTH ABSORBENT painters suite - you can also get suites specific for these types of applications but they usually cost a little more, and since hopefully it will be a one time use, a disposable should work just fine), make sure if your respirator isn't World War III status and cover your eyes, that you wear goggles, and make sure you wear chemical grade protective gloves signified usually by their pH capacity (and learn how to take them off properly so that you don't just contaminate your hands in the end like an idiot - Something I would suspect that someone that things PM is systemic might do)
However, for clippings it is risky. I would use something simple (like manually cleaning off the plant than spraying with water and hydrogen peroxide - something along those lines - You know, don't be fucking lazy) and save the Eagle20 for a later measure (when the plants are larger and a few weeks into veg - The Eagle20 won't protect them forever, they will grow, the new growth won't have any help, and considering that just might be a skilled PM farmer, you will end up spraying it again anyways - So, it is best to wait and provide protection that will last through flowering). Just keep an eye on them.
Eagle20 will chemically castrate you and make your children three-eyed-"I think PM is systemic"-mongols if you don't get cancer first. Never spray it late in the veg cycle. In order to be even rationally appropriate about it you can't spray it within 45 days of harvest, and in reality since they are not apples you are going to wash and polish, that number should really be 60 or more. If your babies are so powdered and fucked up that its not even rational to try to keep them, throw them away and start a new life. A life where you have taken the proper steps to rid your PM production. Eagle20 works - But so does not being a fuck up.
I have only had one problem with PM in my history, which was given to me like herpes from an idiot (one of those people that think its systemic I bet). I used Eagle20 one time and took some other steps and it never impacted me again, because I don't produce those situations, and I know what the fuck I am doing (I swear to God people just never get it. Read something, like... At the library... Maybe find a real life mentor that knows what they are doing - and if they have problems and fixes for them - they don't know what the fuck they are doing. Find someone that has learned to grow without problems, not take chemical short cuts because their still an amateur coping).
One thing to remember is that you have to carefully treat and clean your room (between every cycle. If you are growing in your closet or something - If you don't have a real space that can actually be properly cleaned, stop growing, or just accept the fact that growing in a closet isn't pro status no matter how hard you try - Its an amateur situation so expect amateur problems. And don't spray Eagle20 anywhere in your home or over a carpet, ffs). Beyond that, you should reconsider the configuration of your space, look for issues, and so on. Sometimes, a simple dehumidifier can go a long way in dealing with these types of infections (I have never had bud rot but the idiot that gave me the PM has, but thankfully, he installed a dehumidifier and stopped suffering bud rot - He also said it all but prevented and killed his PM problem... Just think... Its just a little box you plug in... AWESOME!). Air flow is important. Humidity is important. Cleanliness is important. Removing infected leaves is important (and weak leaves. Weak plants - Plants not taken care of... Underfed or whatever the case may be, will invite pests and issues quickly. Remove damaged leaves before they become damaged and infected leaves, ready to pass their STD to healthy leaves).
I cleaned my room by doing the following: After harvest I removed the glass from my hoods and killed the ducting (in-line fan). I than sprayed the floor and walls with hydrogen peroxide. I than scrubbed the walls down with dish soap and water (and the hoods, the fans, the ceiling, the floor.. well.. you get the point). I remembered why I keep my tools in rubbing alcohol. Than, I turned the lights on (again without any cooling) on a hot day (it was nearly 100 out), I kicked on the portable heater on full blast, turned off all of the air circulation, and locked the door. I waited until the temp read 130 for about 4 hours. I kicked on the fans and opened the door and let it cool. Than, I did it again the next day for 4 hours. Than, sprayed my 3 week old new babies (which showed no sign of PM, but that it only takes one spore you can't see) with Eagle 20, separated them, and let each one mature for another week, watching each one closely. I threw away everything replaceable - Pots, twisties, scissors, goggles, gloves, bamboo (the bamboo fucks a lot of people over, they just don't think of it!), and I enjoyed a sense of "new" (I love that new grow room smell!).
I am writing this for anyone that comes this way later on. I was trying to find the answer to this question specifically, "Can Eagle20 stall or damage rooting" - This popped up in Google. My friend that handed PM to me that one time on a Northern Lights platter (if you will) has mostly learned to not be a PM farmer - But now he wants to "save" that strain (and the Mother is not doing so hot - go figure, hes been trying to use 'natural remedies' to deal with the PM issue for a long time now... Making this poor plant suffer over and over again) - So, he wants to know if he can use it the instant he takes the clippings or not (and make two of them Mothers... Though, I don't know why, that Northern Lights he has didn't impress me in the slightest - If I was him I would just fucking move on). My thought was that I would wait until I had root first - But that is just my opinion so I was looking for others.
Have a nice day.