Files being created - Is referring to the file when it was in a state of being created. So once it's fully created, it's no longer relevant.
Files created - Refers to files that is fully created.
flow would go like "not created" -> "being created" -> "created"
So to sum up, in your specific sentence, "Files being created..." says they shouldn't be removed while they are being created, but after your done it's fine to get rid of them. Whereas if it had been "Files created...", then they should never be removed, even your done with the compaction / flush process (could be for logging purposes for instance, if you need a reason why that could make sense)
"That the seas are being overfished has been known for years." the seas are the primary subject, and the fact they are being overfished has been known for years.
"That the seas being overfished has been known for years." overfished
becomes a defining part of the seas. So of all the seas, we're
specifically talking about the overfished ones. So here what we have
known for years are actually talking about the overfished seas, and
not the fact they are overfished.
"That the seas overfished has been known for years." False sentence, can still be understood, but as something like slang.