it is not a problem with FOP2, but your asterisk configuration and the tools you use. When you remove a voicemail from an EXTERNAL application, asterisk is not notified of such action, so it does not broadcast the state, so FOP2 does not get the information. You can somehow make it better by configuring your /etc/asterisk/voicemail.conf to do the voicemail polling:
pollmailboxes = yes ; If mailboxes are changed anywhere outside of app_voicemail,
; ; then this option must be enabled for MWI to work. This
; ; enables polling mailboxes for changes. Normally, it will
; ; expect that changes are only made when someone called in
; ; to one of the voicemail applications.
; ; Examples of situations that would require this option are
; ; web interfaces to voicemail or an email client in the case
; ; of using IMAP storage.
;
pollfreq = 30 ; If the "pollmailboxes" option is enabled, this option
; ; sets the polling frequency. The default is once every
; ; 30 seconds.
Or, you can use fop2 with the voicemail explorer feature that will update fop2 correctly when you remove voicemails with it.
Best regards,