Before we go to the troubleshooting, keep in mind that the slash commands are still in Beta on MEE6, where some inconsistencies are expected (you can always use the legacy version of the command such as !rank).
Solution 1: Basic
Level 1 - Works with or without a Custom Bot™
1. Visit your dashboard and select your server. Now, open the Settings and, at the bottom of the page, turn the Slash Commands off. Wait 24 hours and turn it on again.
2. In case the first step did not work go to the plugin not showing up in Slash List, scroll down to the commands, and turn them all off. Wait another 24 hours and turn it on again.
For example, if you can't find /rank and /levels, go to the Levels plugin and turn off rank and levels commands, wait half an hour and then turn it on again.
3. Now, if the first two steps didn't help, go to your dashboard's settings and turn off the Slash Commands. Next, go to your server, right-click MEE6/Custom Bot and kick it from your server, and then re-add it via your dashboard. Wait 24 hours and turn the slash commands on again.
Note: All information will remain saved during the third step.
Solution 2: Developer Portal Basic
Level 2 - Works only with a Custom Bot™
4. Visit the discord developer portal and select your application (aka Custom Bot). Next, open the Bot tab and make sure all the 3 options under Privileged Gateway Intents are turned on, if they are not, enable them.
Note: Do not enable code to require.
Now, scroll up and regenerate/reset the token. Next, copy the new token, and make sure you do not have Window Popup Blocker enabled on your browser settings (Discord uses it to invite your custom bot back). Then visit your dashboard and click on MEE6 blue face and paste the new token, invite it and it should all be done.
Note: Keep in mind that if your server has 2FA (you can check by visiting the server settings -> Moderation -> bottom of the page) you will need 2FA enabled on the Discord Account owning the Custom Bot's as well (discord disables a lot of features when it's not synchronized).
Try Level 1 troubleshooting now and it should work.
Solution 2: Developer Portal Advanced
Level 3 - Works only with a Custom Bot™:
5. Visit the discord developer portal and select your application. Now, go straight to OAuth2, select URL Generator and select the following, on the top option:
And then, at the bottom option:
Once the new link is generated, copy it and paste it into your browser. Then, invite your bot (yes, we are "double inviting" it) by authorising it again and you should have your problem sorted.
Note: Be careful not to update the commands too often as discord only allows 200 slash commands updated per day.