Mailboxes are not appearing in HC panel.

I also fell into the same trap where my Exchange mailboxes were not listing in HC panel after I ran the Exchange Import tool. The following set of instructions were provided to me by the HC Support team and this might help you too:
 

1. Connect to your Exchange server through RDP:
2. Go to command prompt and navigate to the path: X:\Program Files\HostingController\Web\Bin
3. Execute this query:  HCDBChanges.exe sync_mailboxes <OU_Name>

I hope, I was helpful , please mark my post as helpful, if it really helped you.
 
Inspirational Quote: "Start by doing what's necessary; then do what's possible; and suddenly you are doing the impossible." ( Francis of Assisi )

Yes specific mailbox can also be synchronized inside HC9 panel by following the steps given below:

1. Login as reseller/webadmin in HC panel.
2. Navigate to the menu: Hosting Services :: Hosting Services :: Manage Exchange :: Exchange Enabled Organizations :: Mailboxes.
3. Here search mailbox by providing complete email address of mailbox which you want to sync in HC panel.

Using above mentioned instructions, you will be able to sync the specific individual mailbox in an organization with HC panel.