The following occurred when the linked resource is in portrait orientation but the APhoto2 document is landscape:
1.) Launch APhoto2 2.0.0
2.) Uncheck "Automatically update linked resources..." in Preferences
3.) Create new document: 18x12, 300 dpi, Prefer Linked
4.) Save as Collage-New.afphoto
5.) Drag and drop File2.jpg into document from Windows Explorer. It appears in Resource Manager as a linked resource as expected
6.) Resize and position the image
7.) Save collage. All is well so far.
8.) Edit the linked jpg with an external editor and save it (I changed only brightness and contrast)
9.) APhoto2 notifies that a linked resource has been updated.
10.) Click Update in Resource Manager
11.) Image is updated but rotated 90 degrees clockwise.
In this case, the linked image file2.jpg is in portrait orientation whereas the collage I'm trying to make is landscape.