Hi fordtech 2008,
If the bubbles are small and stable in size, you might just leave them alone.
If you want to do something about them, you might consider puncturing the bubble, possibly injecting adhesive, and applying a Dicor patch. Since patches on the roof might affect resale/trade-in value, you need to consider how long you plan on keeping this trailer.
Replacing the entire roof would be a very radical fix. The rubber membrane is ripped up, damaging the luan layer to which it's glued. A new luan layer is put on, followed by a new membrane. The A/Cs, ladder, vents, skylights and everything on the roof have to be removed and reinstalled. The front/rear caps will likely not be removed, so a new seam will be created at front and rear caps, creating possible future trouble spots.
You might want to call Heartland Customer Service to discuss. Take a few good pictures ahead of time using a reference object next to the bubble to provide a sizing reference. A dime next to a dime-sized bubble would work. You can reach Heartland at 877-262-8032. Have your VIN# ready.