Hi Roland,
Customizing a BSP mainly modifies the source files in the /mqx/source/bsp/<Board Name> directory. When migrating to a different MQX version, what I would do is a comparison of the original BSP that was cloned between the versions. For example, if your CustomBSP was a clone of twrk60d100m BSP, those BSP files are included in both MQX v4.0 and v4.1. Do a diff between the two versions, find any differences done in v4.1, and merge those changes into your CustomBSP if they apply. And if you've modified any other files in MQX, you can do the same. And don't forget user_config.h
Thanks