Dear @deprezal,
Thank you for your message. Please find hereafter some clarifications.
Sen2Cor automatically handles the reading of L1C image bands before and after the change of processing baseline (25/01/2023). So there is nothing to do in Sen2Cor code, neither in L1C pre-processing.
The change that occurred with processing baseline (PB) 04.00 is related to the way the reflectance data is encoded in the JPEG2000 files in unsigned integer.
The only changes you need to make is in downstream applications when converting L2A JPEG2000 images in L2A surface reflectance in order to obtain a floating point value, usually in the range [0,0 ; 1.0]. That is when it is important to use the adapted conversion formula, for example to get consistent NDVI time series like other users reported. Please check the point 4) of the Frequently Asked Questions
We hope you find these clarifications useful.
Cheers,
@Sen2cor_dev_team