This question probably was already asked thousands of times, yet I could not find any similar question.
One creates a software. An innovative one with lots of fancy new things which were never applied. Lets say, a networking system between Earth and Mars on top of SMTP. That software is fully FOSS, and as such is probably financially poor and its devs have no money to patent things they do.
Some years later, one does patent the same method of networking as something generic, such as "Interplanetary networking on SMTP". Does the former need to cease to exist if the one who made the patent demands pay? Also don't forget there's almost no money to fight in court.
PS: Nobody would build a networking system on top of a mail transfer protocol, make it a "something which nobody ever made" sort of thing.