Hello,
For your categories tree : have you use the "Rebuild" function ?
You can find it, here in Components => HikaShop => Categories.
For your listing product display : several points can leads to this, and
maybe your categories tree issue can be linked to this.
But if you succeed to rebuild your categories tree and that
don't solve your displayed issue can you provide a screenshot of your related item menu configuration and more especially your
Categories Options tab ?
Awaiting news from you.
Regards