Oxford nanopore promethion; does guppy3 separate fast5 into pass and fail? If not what does?
Only if they've enabled the --qscore_filtering flag when using Guppy; this flag isn't enabled by default when running Guppy from the command line.
It's a good idea to use all fast5 reads for recalling, because accuracy improves over time, so some that previously failed may slide into the pass folder.
FYI, I'd be much happier if people asked their nanopore sequencing questions here. It's a publicly-accessible website which is indexed by search engines, so makes it easier to find answers, and easier to see the answers when found (i.e. no login needed).
Note that when recalling, you set the input and output directories (I think via the -i and -s flags). These should be different directories, and ideally different output directories for each recalling attempt, to avoid duplicate file entries. The original fast5 files shouldn't be modified by recalling as long as the input and output directories are different.