The IceCube Neutrino Observatory has successfully detected high energy astrophysical neutrinos, providing a wealth of both astrophysical and particle physics information. With the Gen2 upgrade, an increase in scope of observation of high energy astrophysical neutrinos, over a wider range of energies than ever before is to be expected. This will provide unprecedented capability to test for neutrino self-interactions, which may be connected to open cosmological tensions, off the cosmic neutrino background by looking for features in the spectrum. These analyses, however, may be sensitive to the assumptions of the unknown initial flux of neutrinos from the as-of-yet unidentified sources. We investigate the impact of such modifications on these new physics scenarios.