It's possible to fix, but will require a little work. The command to remove stuck enchantments is
player.dispel . In this case, the ID depends on both your load order and which level version of the boots you have.
The IDs are -
xx000DE1 (Level 1-6)
xx000DE0 (Level 7-10)
xx000DDF (Level 11-15)
xx000DDE (Level 16 - 20)
xx000DDD (Level 21+)
The 'xx' is Knights.esp's place in your load order - in hex. Easiest way to find this is probably to use one of the mod managers. If you have Wrye Bash, just look at the load order column. In OBMM, hover your cursor over Knights.esp and look what it says under FormID. If you have neither of those, you can find it in game by opening the console and clicking on something that was added by KotN, like the priory or some of the furniture in it, and looking at the first two digits of the ID displayed at the top of the screen.
So, for example, if you had the best version of the boots and KotN is fifth in your load order, the command would be player.dispel 05000DDD.