I went ahead and disabled the identifyObsoleteKernels function and here is the relevant part of /var/log/dist-upgrade/main.log:
2019-06-19 15:37:29,707 DEBUG Obsolete: libisl19 libpoppler85 linux-headers-5.0.0-13 linux-headers-5.0.0-13-generic linux-image-5.0.0-13-generic linux-modules-5.0.0-13-generic linux-modules-extra-5.0.0-13-generic 2019-06-19 15:37:29,707 DEBUG Foreign: 2019-06-19 15:37:29,707 DEBUG forced_obsoletes: ['desktop-effects', 'gnome-app-install', 'policykit-gnome', 'gnome-mount'] 2019-06-19 15:37:30,001 DEBUG Unused dependencies: libisl19 pppconfig ifupdown libpoppler85 pppoeconf 2019-06-19 15:37:30,001 DEBUG remove_candidates: '{'libisl19', 'linux-image-5.0.0-13-generic', 'gnome-mount', 'policykit-gnome', 'desktop-effects', 'linux-modules-5.0.0-13-generic', 'pppconfig', 'linux-modules-extra-5.0.0-13-generic', 'gnome-app-install', 'libpoppler85', 'ifupdown', 'linux-headers-5.0.0-13', 'linux-headers-5.0.0-13-generic', 'pppoeconf'}' 2019-06-19 15:37:30,001 DEBUG Start checking for obsolete pkgs 2019-06-19 15:37:30,100 DEBUG skipping running kernel pkg 'linux-image-5.0.0-13-generic' 2019-06-19 15:37:30,100 DEBUG 'linux-image-5.0.0-13-generic' scheduled for remove but not safe to remove, skipping 2019-06-19 15:37:30,101 DEBUG skipping running kernel pkg 'linux-modules-5.0.0-13-generic' 2019-06-19 15:37:30,101 DEBUG 'linux-modules-5.0.0-13-generic' scheduled for remove but not safe to remove, skipping 2019-06-19 15:37:30,198 DEBUG skipping running kernel pkg 'linux-modules-extra-5.0.0-13-generic' 2019-06-19 15:37:30,198 DEBUG 'linux-modules-extra-5.0.0-13-generic' scheduled for remove but not safe to remove, skipping 2019-06-19 15:37:30,720 DEBUG skipping running kernel pkg 'linux-headers-5.0.0-13-generic' 2019-06-19 15:37:30,721 DEBUG 'linux-headers-5.0.0-13-generic' scheduled for remove but not safe to remove, skipping 2019-06-19 15:37:30,822 DEBUG Finish checking for obsolete pkgs 2019-06-19 15:37:30,861 DEBUG The following packages are marked for removal: linux-headers-5.0.0-13 ifupdown linux-headers-5.0.0-13-generic pppoeconf libisl19 pppconfig libpoppler85
So just removing the function seems like the best way forward.
I went ahead and disabled the identifyObsolet eKernels function and here is the relevant part of /var/log/ dist-upgrade/ main.log:
2019-06-19 15:37:29,707 DEBUG Obsolete: libisl19 libpoppler85 linux-headers- 5.0.0-13 linux-headers- 5.0.0-13- generic linux-image- 5.0.0-13- generic linux-modules- 5.0.0-13- generic linux-modules- extra-5. 0.0-13- generic app-install' , 'policykit-gnome', 'gnome-mount'] image-5. 0.0-13- generic' , 'gnome-mount', 'policykit-gnome', 'desktop-effects', 'linux- modules- 5.0.0-13- generic' , 'pppconfig', 'linux- modules- extra-5. 0.0-13- generic' , 'gnome- app-install' , 'libpoppler85', 'ifupdown', 'linux- headers- 5.0.0-13' , 'linux- headers- 5.0.0-13- generic' , 'pppoeconf'}' image-5. 0.0-13- generic' image-5. 0.0-13- generic' scheduled for remove but not safe to remove, skipping modules- 5.0.0-13- generic' modules- 5.0.0-13- generic' scheduled for remove but not safe to remove, skipping modules- extra-5. 0.0-13- generic' modules- extra-5. 0.0-13- generic' scheduled for remove but not safe to remove, skipping headers- 5.0.0-13- generic' headers- 5.0.0-13- generic' scheduled for remove but not safe to remove, skipping 5.0.0-13 ifupdown linux-headers- 5.0.0-13- generic pppoeconf libisl19 pppconfig libpoppler85
2019-06-19 15:37:29,707 DEBUG Foreign:
2019-06-19 15:37:29,707 DEBUG forced_obsoletes: ['desktop-effects', 'gnome-
2019-06-19 15:37:30,001 DEBUG Unused dependencies: libisl19 pppconfig ifupdown libpoppler85 pppoeconf
2019-06-19 15:37:30,001 DEBUG remove_candidates: '{'libisl19', 'linux-
2019-06-19 15:37:30,001 DEBUG Start checking for obsolete pkgs
2019-06-19 15:37:30,100 DEBUG skipping running kernel pkg 'linux-
2019-06-19 15:37:30,100 DEBUG 'linux-
2019-06-19 15:37:30,101 DEBUG skipping running kernel pkg 'linux-
2019-06-19 15:37:30,101 DEBUG 'linux-
2019-06-19 15:37:30,198 DEBUG skipping running kernel pkg 'linux-
2019-06-19 15:37:30,198 DEBUG 'linux-
2019-06-19 15:37:30,720 DEBUG skipping running kernel pkg 'linux-
2019-06-19 15:37:30,721 DEBUG 'linux-
2019-06-19 15:37:30,822 DEBUG Finish checking for obsolete pkgs
2019-06-19 15:37:30,861 DEBUG The following packages are marked for removal: linux-headers-
So just removing the function seems like the best way forward.