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Reprocessing pn data with SASv6.0.0 yields event lists with less photons than with SASv5.4.1. Am I doing something wrong?

You are probably not doing anything wrong, but your SAS is. After release of SAS v6.0.0, it has been discovered that in a small number of observations (mostly clustered before Rev.#206) an OAL call in epframes may erroneously return NULL event times. This problem occurs on most software platforms, except True64Unix.

This problem can be easily identified. On exposures affected by it, the warning InvalidObtValue is generated during the processing.

This will be fixed with a software update, available in future SAS versions. Unfortunately, there is currently no workaround available. If this problem occurs, you should process the affected pn exposures with SAS versions older than v6.0.0 (indeed, it is enough to run the SAS v5.4.1 epframes, and then, for instance, re-use the output files in a subsequent epchain run, specifying the parameter runepframes=N).