I just stumbled across this post from 2 weeks ago. This response is my opinion only.  Many owners like to re-torque the head bolts from time to time, including the nuts a 6 and 12 o'clock which are not located under the rocker cover.  That requires all the nuts to be  loosend . If I had 1 messed up rocker arm, I would be tempted to change just that one part. However, if you are changing both, just get it over with. 25 ft/lb is the generally accepted torque value. I would arrive at the final torque in 3 steps. (say like 9,18,25) Be aware that the long studs can fail where they are threaded in to the motor casting. I experienced that failure on the left side of a 1988 R100RS I used to own. 

Hello Richard,

i am new this community, i have a 1988 bmw r100rt which i got couple of months back.. were you able to replace the rocker arms? Did you replace both? I have some questions if you dont mind

My take on this is that it all depends.   What is the reason to replace?  What do the others look like?  As long as the valves are adjusted properly there should be no problem.

As for removing the nuts, no Problems there.  These are not one time torque and throw out bolts.  They are OK to loosen and retorque.   I would loosen the two remaining head nuts a half turn and tighten all of the six in the proper pattern to proper setting.  St.