MacCulloch's work on the Reformation has a bit of information, though it's not enough to fully answer the OP. During the 15th Cent, two things happened to make texts more accessible: because of the Turk's occupation of the East, Christians fled to the West, bringing manuscripts with them. The second thing was printing. I agree that it's speculation, but I think it's a fair guess that the answer to the OP was changing during the period of the Reformation, with printed editions appearing during that timeframe.
Here's a work reviewing Calvin's use:
John Calvin and the Church Fathers It says "it may be first remarked that, during Calvin's lifetime, nearly all the important patristic texts had become available in printed editions. Above all, this work was carried out by Erasmus, but important work was also done by other Christian humanists like Faber Stapulensis, Beatus Rhenanus, Pirckheimer, Clichtoveus, Beraldus, Gerbellius, and by contemporary Reformers such as Pellikan, Oecolampadius and Musculus. Next to their editions of the various texts (at first the Greek Fathers were usually published in Latin translations), editions of the general Church councils and of the councils of Africa were also available. Calvin, for instance, made frequent use of Petrus Crabbe's two volumes
Concilia omnia, tamgeneralia, quam particularia...(Coloniae, 1538)." It goes on to note that it's not clear whether he consulted manuscripts personally. He might well have found everything he needed in published form, particularly for the later editions of the Institutes.
The works I see listed in that paper are all "orthodox." It's less likely that he had access to recently published unorthodox works such as the Gnostics, Nestorius, etc. He probably wouldn't have used them anyway.