Thank you for your message.
The most likely issue is that the JoyCon is reconnecting to the Switch rather than entering pairing mode.
It is also worth noting that you can’t pair both JoyCon halves at the same time, you’ll only be able to use a single JoyCon. There are third-party software solutions that supposedly resolve this, but we do not support them.
If the iPhone is able to be paired, there shouldn’t be any configuration that is blocking the discovery of the JoyCon from the PC side, any issues are likely related to the JoyCon’s actual discoverability.
I hope this helps.