In bubble assisted vacuum thermoforming, measuring pressure-induced mechanical strains through the stereo-digital image correlation (stereo-DIC) technique while shaping thermoplastic sheet requires consideration of an appropriate reference state of surface deformations. However, when the stereoscopic measurements can be only performed after the heating step, the correlation problem should be well-posed otherwise the reliability of results is limited. This study focuses on stretching by bubble inflation processes following thermal warpage and sagging of initially flat sheets. For this purpose, an experimental rig is instrumented to heat high impact polystyrene (HIPS) sheets and to perform synchronized pressure and stereoscopic measurements during 1.5 s stretching. A two-step method is introduced to separate mechanical strains which are affected by the uncontrollable change of initial conditions from the global stereo-DIC strains. The first step relies on amplification of damped oscillations at the initiation of the inflation process due to sagging. Out-of-plane displacements confirm the existence of a temperature-dependent characteristic time that marks the transition from the sagged to the strained surface shapes. The second step uses these characteristic times to objectively shift the reference of image-correlation computations. To evaluate the effectiveness of the suggested method, inaccuracy levels of global strains are evaluated at a fixed pressure level under different thermal conditions. It is shown that inaccuracy levels are the highest when stereo-DIC measurements followed warpage and they decrease with amplification of sagging. The developed approach extends the use of in-situ stereo-DIC measurements when changes of initial conditions are uncontrollable and thermal strains cannot be measured.