I'm guessing that although you had downloaded the bonus content you may not have actually loaded them in CTA yet. This would account for them showing as Bonus content.
Verification of downloaded content takes place the first time you use them so normally any content you have used should be ok but any unused bonus content will show the "Get Me" page.
You should be able to go to your Inventory in the Marketplace, select all the content that has a Bonus mark showing and redownload.
If during the download process you are prompted about files with same name then don't choose "No" as this will cancel the process and leave the old content there. Choose "Yes" and then rename each file as prompted. This should do the trick.
Once downloaded successfully you can go into Windows Explorer and manually delete the older "Bonus" content and rename the newer versions if you wish.
Give this a try and see if it helps.