So, you did see them in the currency pouch? It sounds to me like you might have redeemed them for something if they have gone missing.
Try the I can't find the RuneScape Bonds I purchased support page. Click on 'Yes' then click on 'Contact Us' to get to a message form to message Billing Support. Fill out the form as best you can then use the free text box to explain that two Bonds went missing and ask them to check to see if you accidentally redeemed them.
This may seem odd but it seems impossible to contact someone that can help me. I have searched 'contact support ' in the forms and it comes up with people that are facing the same problem as me. it seems that the people who are trying to help have little to no Idea how to do so. Is there an email or a link that you might have?
You need to get your account checked by the Billing Support JMods. They work UK business hours, they don't come into the forums and they can only be contacted via the webforms in the Support Centre.
Please follow the instructions I posted in my first reply - click on the link I posted and follow the instructions posted above. Your webform request goes into a queue to be dealt with but you should be replied to within 48 hours.