Sometimes when there is corruption, mails disappear from the inbox. The following are some solutions:
In some cases, just performing an Updall will fix it.
Other cases, we just delete the $Inbox and then reapply the template.
Finally, we need to actually convert it to another template, convert it back and then delete the $Inbox folder and then reapply the latest template.
The command to convert the template will be like follows (execute from the LN Console):
l convert -s mail\mailfile.nsf * inotes6.ntf