Although the layer transparency is stored within the xdata of the layer table entity and may be used to obtain the transparency of a given layer, if I recall correctly, modifying this xdata has no effect on the transparency of the layer, and so the transparency must be modified using a command call (this may be different in BricsCAD). There is a thread at the Swamp which discusses this behaviour.
Thanks for comfirning it Lee!
Sadly theswamp is still closed, first few days I thought the site was at maintenance process. Now alot of the answers for the lisp questions must be googled somewhere else.
@ Lee:
I think we have discussed this before at http://www.theswamp.org. In BricsCAD you can use entmod to change a layer's transparency. There have been some update issues, but these have meanwhile been fixed. But you do (still) have to regenerate after changing a layer in this manner.