So let me get this straight.
1. You ran a previously used can on a .22lr for 1k rounds.
Yes, it was used. But that is exactly what the OP is asking. Can he run a centerfire can on his 22 and switch back and forth. As stated earlier, centerfire cans dont require much cleaning (especially on a bolt gun). It was not "dirty".
2. Cleaned it in an ultra sonic cleaner.
Correct. Could have done worse by using the "soak" which is corrosive.
3. Fired 5 rounds out of used but now clean can, after it was dry with shitty accuracy. (Shitty groups, POI change, or both?)
As clean as it can get after a 20min soak in the ultrasonic. Groups were opened up.
4. Fired 100 rounds of .22lr though used but now clean can with the exception of 5 centerfire. (Any shitty groups, POI change, or both.)
Groups were opened up.....
5. You can not explain why this was.
I am not a suppressor manufacturer. I own them, I use them, I have experience with many different manufacturers and know some of these companies very well.
6. Fired 4 rounds and noticed and end cap strike.
Yes, 4 rounds of centerfire (308) The baffle strike was not there prior to the 100 rounds of 22 or after the cleaning. So that leads me to believe that carbon buildup played a major role in the damage. And going back to what the OP asked for...... I again say it was a bad idea to go back and forth. A sealed can is extremely difficult to clean adequately to ensure that you have cleared the buildup a 22 can leave behind.
If this is true you really didn't isolate the end cap strike, you just noticed and end cap strike after you swapped you can from gun to gun several times and a cleaning. There are a whole shit ton of things that could have occurred like a chunk of carbon came loose and obstructed the bore of the can. Maybe the threads on your .22 are shorter than on the host gun. If thats the case the threads in the can could have built up with carbon so when you threaded it back on to the host it didn't shoulder up.
Well, here we go again. The OP asked if he went back and forth.... was it good or bad. Given my results..... it was a bad idea. That's my opinion based on actual experience. I'm not ragging on you, Im just not sure you understand the point that is being made here. Groups were sub par in my testing after the rimfire, regardless of the bath because it recreated it after 5 rounds were fired, then 100 rimfire, then 4 more centerfire. We had planned for 100 but heard the familiar strike noise and stopped. Plus the shot went way left of our aiming point.
If it makes you feel any better I got an end cap strike on my SDN-6. Root cause: I used blue locktite on the threads of the brake. Hot barrels soften that stuff up quick. The can cam loose a quarter turn and shitty accuracy and POI changer were realized. Lesson learned: Use provided Rockset. Point being, I isolated the root cause.
Why would you run blue loctite on a muzzle brake that comes with Rockset? That is your fault for not following your user instructions. You can prevent this stuff, which goes right back to what the OP asked for, and what I tested for. Again, not giving you shit. I am just saying why bring the trouble upon your equipment when it can be avoided by reading your manual or following some simple ADVICE.