Ah, thank you for this new information. I was unaware about the bolted connection subassembly structure option. I have been playing around with the PnG I made for this demonstration. It seems that the bolted connection must be created with this structure on or off originally - there is not an apparent way to convert a BC that was not generated this way originally.
What has seemed to (mostly) solve the problem is just selecting the Manual solve option as you have indicated. It solves 2/3rds of the problem, because it updates the connection without having to open and click through a dialog box, and I seem to be able to select multiple bolts in the feature tree, RMB->Component->Manual solve and it will update everything selected. I am still slightly confused as to why this wouldn't be included inside a refresh subroutine deep in the code.
It is also a bit odd that in this selection menu there is a checkmark present (or lightening bolt indicating a needed update) as if this option is currently enabled next to the manual solve option, and regardless of how many times I select this option it will not clear the checkmark - it seems to be not un-selectable as a menu option, it seems to act more like a button hidden inside a drop down menu. It is interesting though because the problem occurs originally when the BC is generated (basis of my problem). If I click through and (try to) uncheck the 'manual solve' option, the problem disappears, but the manual solve checkmark doesn't change (as described above). If I repeat this process again, the problem returns.
It is as if the checkmark is stuck on, but the 'manual solve' option is in fact originally off (though shows as on), then gets actually turned on and fixes the problem in the second iteration of the test process, then gets turned back off in the third iteration of the test process(though still shows on) and the problem returns - all the while the checkmark for the manual solve option is present (showing on).
Not sure where to go from here, maybe someone can look into the code that shows that checkmark as displayed or not, it seems to be faulty and shows always on.
I can accept it as a work around as it seems to work in the large model I was working in when I discovered it. Checking the 'manual solve' option after selecting all the bolts that require the update starts an automatic string of processes that renders the computer and inventor un-useable and seems to take 2-3 times longer amount of time that individually opening each bolt and clicking through would - but it is done in the background meaning I can select all 200 something bolts and start the process, and then go to lunch or come back the next morning while the program crunches - somewhat of a workaround ...somewhat. In our field it is not uncommon to leave a computer crunching overnight to perform large pipe flow calculations, generate point clouds, or calculate FEA outcomes, I just didn't forsee it being necessary while updating bolted connections.🤷
Thank you all for your time and effort.