There’s no publicly released evidence that the Parchin military base has anything to do with Iran’s civilian nuclear program – but proving it isn’t would require many, many IAEA visits, something Iran has rejected.
That’s because IAEA visits to military bases are not obligatory in the first place, and unrelated data collected by the IAEA has a nasty way of ending up getting leaked to Western nations, which means letting the IAEA wander around the base is tantamount to opening a big part of Iran’s conventional military arsenal to foreign spies.
It’s possible though, according to Iranian Deputy FM Hassan Qashqavi, that IAEA visits would be allowed: if the US and Israel weren’t constantly threatening to attack Iran.
Constant threats of attack are a big reason for Iran to keep their retaliatory capabilities a secret, meaning opening up a missile base like that would be difficult to justify. At the same time, both the US and Israel threaten Iran so casually these days that it is hard to imagine it will stop, meaning the site is likely to remain closed.