I have a very short waveform, too short to resolve accurately on my scope.
So, you don't actually know what the shape of the waveform is with any accuracy, since you can't see it. How would you calculate the RMS value of a signal you know nothing about.
When I expand the waveform, the RMS of one complete pulse is 6.6 Vrms, 0.000 001 2 seconds long.
So, now somehow you are able to resolve the waveform accurately? Where did the Vrms value come from now? Are you perhaps talking about a literal square pulse that has 6.6Vpp amplitude and 12μs length?
Nothing about the question makes much sense to me.
The answer appears to be as follows...
A 6.6 Vrms 0.0000012 second pulse, in a 0.0000012 second (833,333.33 Hz) time period would be 6.6 Vrms because the pulse fills the time period 100%.
The RMS value is always measured over some time period, and you're only converting between two values by scaling them with time. The original RMS value must also be attached to a time period. It has no meaning otherwise if the signal is non-periodic, like a single pulse would be.
An aperiodic signal with 6.6Vrms calculated over 1.2μs interval will maintain its rms value if you "translate" it to... the same time interval. That's by definition - nothing much to see here.
A 6.6 Vrms 0.0000012 second pulse in a 0.000254 second (3,3937 Hz) time period should be approx 0.399 Vrms.
A 0.000'254s=254μs period is equivalent to the frequency of 1/254μs=3937Hz, not "3,3937". It's much better to type using reasonable metric magnitude suffixes and avoid too many decimals, whether zero or otherwise. It's too easy to have typos otherwise.
A 6.6Vrms aperiodic signal measured over a 12μs interval, with zero value outside of the interval, will measure \$6.6\cdot(12/254)=0.31{\rm\,V}\$ over the interval of 254μs, not 0.4V as you stated.