Generally when she's done she's done. The whole plant.
I have heard of sativas being harvested as they rippen, as they take so feckin' long to flower. Yours is obviously sativa, but I hardly ever grow them so couldn't say about harvesting in stages..
You will probably find it all rippens at the same moment, hence the need to expose buds now.
In answer to your question; Yes, it will stress them out if you chop the main colas... unless they are ready (which seems unlikely imo)