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Played around all night and couldnt figure it out. Luckily by reading though the countless questions on their FAQ page this morning, I found the answer. I havent tried it yet, but hopefully it helps anyone else having the same issue.
"5.14. How can I use exactly the same stitching settings for different sets of images?
This can be useful for creating HDR panoramas, where the bracketed exposures have been taken in identical orientations, or for stitching panoramas that were taken with an exactly reproducible setup (using a panorama head with accurate click stops).
To stitch multiple panoramas with the same settings, the Apply Template function can be used (also see Q2.13). Create the first panorama in the regular way and save the project file. For the subsequent panoramas do the following:
Start a new project
Load the source images
Switch to Advanced mode by pressing the Advanced button in the Project Assistant
Choose 'Apply Template' from the File menu and browse to the project file saved earlier
Go directly to Create Panorama to stitch the result. Don't add any control points and don't press Align Images"
"2.13. What does 'Apply Template' do?
This copies the settings of another project to the current project, except for the images and the control points. This function is accessible both from the 'Apply Template' item in the File menu, and from the toolbar in PTGui. A template can be any PTGui project. In Tools/Options/Folders&Files, a folder can be configured where you store your templates (on Mac go to the PTGui menu, Preferences, Folders&Files). Then, the template selection dialog will by default open in this folder. There's a little triangle button next to the 'Apply Template' button on the toolbar, which shows a drop down list of all templates in the configured template directory, for quick access.
Templates can be useful for a quick initialization of a project (lens settings, rough alignment of images), although this is usually not necessary since the Project Assistant can figure out the alignment of the panorama by itself.
Another use for templates is when you have an exact reproducable setup (high quality panoramic head with fixed angles). In this case you could copy all settings of a previous project and there would be no need for placing control points and optimizing.
By default, applying a template copies all settings from the template to the current project except for the source images and the control points. In PTGui Pro this behaviour can be modified in the Project Settings tab, section 'template behaviour'."