This study aimed to analyze the potential occurrence of dentinal defects after the removal of a root canal filling with two different sealers using Reciproc (RC) or Reciproc Blue (RB). The mesial roots of 60 mandibular molars with a Vertucci type IV configuration were selected. The samples were initially instrumented with Reciproc (R25) and then divided into the following four experimental groups according to the endodontic sealer and retreatment instrument (n = 15): BC Sealer/Reciproc (BCRC); BC Sealer/Reciproc Blue (BCRB); AH Plus/Reciproc (AHRC); and AH Plus/Reciproc Blue (AHRB). Then, the samples were scanned under micro-CT after obturation and removal of the filling material. Two analyses were conducted. First, an evaluation was performed on all the axial images, and another analysis evaluated each millimeter of the 10 mm from the apex. Dentinal defects were observed in all the samples. All of the identified defects in the images after filling material removal were present in the corresponding images after obturation. The use of AH Plus and EndoSequence BC Sealer, and filling material removal using RC and RB instruments did not induce dentinal defects.