This paper introduces an extension of the thermal error compensation based on the Torque Limit Skip (TLS) to two independent spindle systems of a multi-spindle Swiss-type lathe. The TLS method is a recently introduced approach for the measurement and compensation of thermal errors of precision machine tools. Until now, this method had been used for probing at a single location and to create a single compensation model, specifically on the main spindle of a Swiss-type lathe. The challenge of a second counter-spindle system is that it introduces a second tool-center-point into the working space, the thermal behaviour of which is different compared to that on the main spindle. Furthermore, on Swiss-type lathes, there is no possibility to measure with a movable touch-trigger probe or displacement sensors. This work therefore extends the TLS compensation to the counter-spindle, by devising a second probing location and implementing a second compensation model. It is demonstrated that the two measurement cycles and compensation models can run independently and that each model can compensate the thermal errors of its corresponding spindle system. Results show that with out-of-sync operation of the two spindles, the TLS measured thermal errors are reduced by 80% when using a compensation model based on transfer functions.