There is a specific condition when Calendar items will be removed from the mailbox after being archived. 

When the Mailbox policy is configured to NOT create shortcuts and delete the original item, the archive task will remove the calendar item from the mailbox post archiving.

This setting in on the Archiving Actions tab of the Mailbox Policy properties.

Under this configuration, the workaround is to use an EVPM script against the Calendar folder.  For information on how to run EVPM please review the Utilities Guide in the Related Articles.

The following EVPM script can be modified to match the archiving rules in the environment:

[Directory]
directorycomputername = EVSERVER
sitename = EVSITE

[Filter]
Name=Calendar
CreateShortcut=False
DeleteOriginal=False
UnreadMail=true
UseInactivityPeriod=true
InactivityUnits=Days
InactivityPeriod=60

[Mailbox]
distinguishedname =  /o=EVSITE/ou=Exchange Administrative Group (FYDIBOHF23SPDLT)/cn=Recipients/cn=User 1

[Folder]
Name = Calendar
FilterName = Calendar
OverrideArchiveLocks = True

Note: Before Post Processing, specially when safety copies are set to be removed after backup, a duplicate Calendar item will be seen in the mailbox. However, this item will be removed after Post Processing.