Perhaps a naïve question, but what would an EMP do to ones brain/CNS?
I don't know the results for humans but a study on rats showed that multiple exposures to 200 kV/m would cause minor damage to veins in the brain.
https://pubmed.ncbi.nlm.nih.gov/19725471/
And an article about if EMP could damage human brains:
https://www.scientificamerican.com/article/could-certain-frequencies/
To summarize I don't think your body or brain function would be affected, but your body (skin for example) might get damaged just like a microwave could burn you.
I imagine it's the same as radio frequencies we use regularly (like your phone/wifi), those you don't notice either. And the EMP would usually be a single pulse.
Today there was a special about static electricity on LTT & ElectroBOOM! showing how much effort it takes to damage a chip with static electricity. They mention they use 10-20kV and parts are usually rated to withstand 2kV.
Chips in your body would probably we very small, else you would feel them inserted, but they are also in your body which would require more voltage.
Because they are so small it would also require them to be on the location they inserted them, else you couldn't read-out the value easily. Or they need a giant source to power the chip and very sensitive receiver to read-out it's value.
They probably would put the chip into your upper-arm, as usually that's the place vaccines are inserted. So reading them out would also be done at that location (how suspicious if you didn't know and some needs access to your upper arm).
Breaking the chip would then also be done at that location, you probably wouldn't even notice it happened and it wouldn't have any impact on your body.