If by "old 2006 version" you are referring to RadControls for ASP.NET Classic (i.e. RadGrid.dll, RadCalendar.dll), you might not experience any issues from them coexisting with RadControls for ASP.NET AJAX, depending on your setup.
Using controls from both suites on the same page, however, will almost certainly cause issues.
Having that in mind, it would be best if you migrated the "old" controls to their RadControls for ASP.NET AJAX counterparts. Our documentation contains extensive migration articles for each control (example
Let me know if that helps.
EDIT: I corrected my initial statement after checking with another colleague.
the Telerik team
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