Saving the factory file is the standard way of saving how you set up and printed something. Once saved, you can load at any time and be able to do an identical print.
And I think I've spotted a few strange things in your file.
Firstly, I get an error when reading the profiles in. Once for each profile "Failed to parse XML file" This may point to the cause of your problems..but I'm not sure. Clicking OK on each error results in everything loading.
Checking out the two profiles, neither had a model selected. I set one model to each profile.
I then spotted both profiles had rectilinear infill set. I changed one to honeycomb.
On slicing, one had rectilinear infill, and the other had honeycomb infill as I would have expected.
Try loading the attached updated factory file and see if you get a difference. I'd also try loading the factory file you saved to see if you get the same two error messages. If you do, then your original settings may be corrupted.
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