The conflict you are reading about regarding the effect of the bullion shipments on prices is still not resolved among economic historians and may never be.

The argument that bullion shipments from the Spanish colonies caused a "Price Revolution" was originally proposed by Earl Hamilton in 1934. Since then, changes in economic theory regarding money have caused the Hamiltonian argument to be constantly re-evaluated thru almost every price model economists have created. Economists, Historians and Economic Historians are still publishing papers and unearthing data on this issue.

In Hamilton's favor, it's fairly simple and obvious that huge increases in money should have some effect on prices. The 16th century import of silver may have nearly doubled Europe's supply of silver in circulation. The gold supply may have increased by 20%. It's hard to imagine that this had zero effect, and indeed there is an observed increase in prices, especially in Spain.

The problem is that these are not the only things that are going on in the 16th century and there are several competing explanations and problems with data. Firstly the population expanded and became more urban, with many economies becoming cash based (i.e. taxes collected in money and not in produce or service), which greatly increases the rate at which currency circulates. Also, the banking sector greatly expanded which may have driven up the supply of money (a whole separate discussion). And as far as the data goes, the greatest price increase is in the first half of the 16th century (1500-1550) while the greatest increase in silver imports occurs after the 1540s. And of course, there is the simple fact that price level estimates and statistics on bullion imports are very suspect and not wholly reliable for any era in history before the advent of large government statistical bureaus in the 20th century.