Screenshot of my guy's equipment, (slightly doctored so the popup doesn't cover the neighboring slot) He's currently wearing only equipment that requires minor power tokens. His skill requires a minor but is using a major. If I try to swap in a piece of equipment that uses a major token (in this case, putting a Steel Shield in the place of that Parrying Buckler) it does not allow me to because the major token is in use by the skill even though if the swap goes through, it could use the now available minor.
The manager sees that that token is in use and sees that there's none left in the 'pool' It will not be able to make a judgement call on what you're trying to do. Un-equipping an item drops the token(s) back in the pool. It's looks like there's an obvious solution in your example, but if you have multiple major tokens - remember we haven't seen half of them - things may be much more complex. http://wiki.cardhuntria.com/wiki/Power_Tokens
It should be smarter about this and calculate if the new configuration is legal even if it requires reallocating tokens.