Hello andysfd,
If the sub-sets of images which are not connected consist of considerable number of geotagged images, even if you run the Align Photos operation in the single chunk, the result will show several non-connected components in the Model view.
Alternatively you can process (align) images related to each isolated component in separate chunk, then merge the chunks (as all are aligned with each other by default thanks to the georeferencing data) and continue with further processing operations.