You're right, an updated panel will remove your javascript bindings.
In your postback update block, reregister the corresponding javascript.
Sort of:
ClientScriptManager cs = Page.ClientScript;
cs.RegisterStartupScript(typeof(Page), "ReApplyJavascript", "<script type=text/JavaScript>YourJavascriptInitMethod();</script>", false);
If this does not work. You may need to use:
ScriptManager.RegisterStartupScript(Page, typeof(Page), "ReApplyJavascript", "<script type=text/JavaScript>YourJavascriptInitMethod();</script>", false);
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