Recently different experimental schemes have been proposed to study the elusive phenomenon of entangled two-photon absorption (ETPA) in nonlinear materials. The attempts to detect ETPA using transmission-based schemes have led to results whose validity is currently under debate because the ETPA signal can be corrupted or emulated by artifacts associated with linear optical losses. The present work addresses the issue of linear losses and the corresponding artifacts in transmission-based ETPA experiments through a new approach that exploits the properties of a Hong-Ou-Mandel (HOM) interferogram. Here, we analyze solutions of rhodamine B (RhB), commonly used as a model of a nonlinear medium in ETPA studies. Then, by using the HOM interferometer as a sensing device, we first demonstrate the equivalence of the standard transmission vs pump power ETPA experiments, presented in many reports, with our novel approach of transmission vs two-photon temporal delay. Second, a detailed study of the effects of optical losses, unrelated to ETPA, over the HOM interferogram is carried out by: (1) characterizing RhB in solutions prepared with different solvents and (2) considering scattering losses introduced by silica nanoparticles used as a controlled linear loss mechanism. Our results clearly expose the deleterious effects of linear optical losses over the ETPA signal when standard transmission experiments are employed and show how, by using the HOM interferogram as a sensing device, it is possible to detect the presence of such losses. Finally, once we showed that the HOM interferogram discriminates properly linear losses, our study also reveals that under the specific experimental conditions considered here, which are the same as those employed in many reported works, the ETPA was not unequivocally detected.