Depends on how you have set the machine up, but as standard, the machines scan back to their own HDD's. Try checking the copier to see if your scans are being held there. Use the following to check for the scans.
\\CopierIPAdress\File_Share\
If you aren't scanning to the local share on the machine, then you must check which 'Remote' scan location or 'Template' you are using. Once you know exactly which location you are using to scan to, go into TopAccess and have a look at the UNC path either in the Remote scan location or the Template you are using.
If you are scanning to Email, make sure that the machine is authorised to send email through your SMTP server. If it isn't, the machine will report that it sent the email ok, but the server will delete the email presumming it is spam.
Finally, check the 'Log' on the copier. Go to Job Status - Log - Scan and see if there are any errors in the list. If there are, check the Users Manual as these codes are written in there.
Hope this helps.