I'm sorry to hear about issues you've been experiencing regarding this functionality. This is happening because the widgets get associated with the placeholders on the template, and once you change the template the widgets "don't know" to which placeholder to associate, that's why they just become orphaned and don't get displayed. I agree with you that this behavior might be unexpected and cause problems, and we are discussing how we can improve this. Any suggestions are welcome. In the meantime, Lyubomir Dokov provided a sample code which offers a solution to the problem. You can track his reply and get hte code sample on this forum thread.
Please take a look at it and try the proposed solution.
I hope you find this information useful. If you need any further help, please do not hesitate to write back.
the Telerik team