when you cloned the program, did you click refresh icon on audience panel (on control panel) to update the audience number?
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Even if you cloned this the members tab should be empty until after the email has been sent.
As far as I know, Members are leads that are already part of a given Program because they have already been through the flow. I think Audience is only based on the Smart List of new leads that you are targeting. You should be ok.
I did some investigations and asked our users here.
It seems someone tried to import a csv file twice (2000x2) but it went wrong (csv imports can be tricky on Marketo). Even though they deleted the list, they did not delete the leads inside the list.
Every deleted list had the same name as the active one, that might be the reason I had 2000x3 in members, but 2k in Audience/static list. The audience was right as I thought, but I did not notice that my database was infested because of that issue.
I made them delete the incorrect imports and we're good.
Sorry for annoying you with this, I'm glad everything is sorted out.