The invitation in your Inbox and the calendar entry are the same document, you are just looking at it in different ways. That's why when you delete the invite from your inbox it deletes from your calendar.
You have two options:
- The easiest is to go into your Calendar preferences and check the option "Remove meeting invitations from my inbox after I respond to them". In an R5 mail db you will find this on the Autoprocess tab, and in an ND6 mail db you will find it on the Display tab.
- the second option is to use the Remove from folder option (from the Folders button) instead of deleting. This is just a manual version of what the first option does.