In what fashion would a royally chartered city be punished for not upholding it’s feudal obligations (say by refusing, in times of war, entrance too and use of the city by forces loyal to the crown)? – Thank You, RSAFan.

Well, it depends who won and how they wanted to proceed. The City of London, for example, was known for its Yorkist sympathies, but Henry Tudor understood his need for the capitol (and its capital) outweighed any desire for revenge. But losing your charter might be a potential punishment – indeed, the Intolerable Acts passed by the British Parliament to punish Boston for the Tea Party are an 18th century example. 

Worst-case scenario?

Münster

in 1534-5, which was put under siege by its own bishop (the chartered city in this case was part of a prince-bishopric), starved out, and then sacked.