One of two thunderbolt ports not working on 2017 MBP 13inch

My guess is there was some dirt or liquid stuck on the connector in the port. Plugging and unplugging the cable multiple times probably clean the connector a bit so the cable has a better electrical connection now.

Try using another charger and charging cable just in case the problem is with one of those items.

Otherwise I hate to be the bearer of bad news, but you are going to need to have Apple or an Apple Authorized Service Provider provide you with a repair estimate. Since you have the non-Touchbar model the USB-C ports are a part of the Logic Board so expect an expensive repair (expect to pay at least $500 US).

Also, you should check to see if the laptop qualifies for this free Apple SSD repair program:

https://support.apple.com/13-inch-macbook-pro-solid-state-drive-service

FYI, here is the current list of publicly acknowledged free repair programs for various Apple products (some products such as your laptop have multiple programs available):

https://support.apple.com/service-programs

You have some sort of hardware issue. I'm not sure from reading your post whether the other USB-C port is working or not, but it really doesn't matter:

• If one port is working correctly, but the other one is not working correctly, then you have a hardware issue with the I/O ports.
• If one port is not working at all, but the other port "sort of works", then you have a hardware issue with the I/O ports.

Since you have the non-Touchbar model the I/O Ports are hardwired to the Logic Board and will require a Logic Board replacement. You need to have Apple or an Apple Authorized Service Provider examine the laptop to confirm since I cannot see the laptop myself and my diagnosis is based solely on what you've described here.

Raichu0204 wrote:

so there's nothing wrong with the charger, as it charges in the other port.

USB-C cables can fit in two directions. Maybe one way the cable plugs in will work and another way it will not work. It isn't always easy to rule out the cable and charger unless you have another set to test with.

I don't think its a hardware issue, as it works if plugged in before the laptop boots. this means its the operating system when booted stopping it working,

When the laptop isn't booted the laptop doesn't need all that much power. When the laptop is booted it consumes a lot more power. Some part of your hardware isn't able to deliver this extra power needed to run the whole system. My guess is the Logic Board is bad (probably had some damage to the USB-C ports).