Tammann’s two-stage crystal-nuclei-development method is applied for analysis of the thermal stability of homogenously formed crystal nuclei of poly(butylene isophthalate) (PBI) as well as their possible reorganization on transferring them to the growth temperature, using fast scanning chip calorimetry. Crystal nuclei were formed at 50 °C, that is, at a temperature only slightly higher than the glass transition temperature, and developed to crystals within a pre-defined time at the growth temperature of 85 °C. The number of nuclei, overcritical at the growth temperature, was detected as a function of the transfer-conditions (maximum temperature, heating rate) by evaluation of the developed crystal fraction. For different size-distributions of crystal nuclei, as controlled by the nucleation time, there is detected distinct reduction of the nuclei number on heating to maximum temperatures higher than about 90 to 110 °C, with the latter value holding for longer nucleation time. Longer nucleation allows for both increasing the absolute nuclei number and generation of an increased fraction of larger nuclei. Heating at 1000 K/s to 140–150 °C causes “melting” of even the most stable nuclei. While direct transfer of crystal nuclei from the nucleation temperature (50 °C) to the growth temperature (85 °C) reveals negligible effect of the transfer-heating rate, in-between heating to higher temperatures is connected with distinct nuclei-reorganization above 85 °C on heating slower than 1000–10.000 K/s. The performed study not only provides specific valuable information about the thermal characteristics of crystal nuclei of PBI but also highlights the importance of proper design of Tammann’s nuclei development experiment for analysis of nuclei numbers. With the evaluation of critical rates of temperature-change for suppression of non-isothermal formation of both nuclei and crystals, the kinetics of crystallization of the slow crystallizing PBI is further quantified.