diff --git a/src/calibre/gui2/viewer/web_view.py b/src/calibre/gui2/viewer/web_view.py
index b5e2553897..6c7298d564 100644
--- a/src/calibre/gui2/viewer/web_view.py
+++ b/src/calibre/gui2/viewer/web_view.py
@@ -153,12 +153,9 @@ class UrlSchemeHandler(QWebEngineUrlSchemeHandler):
             return self.fail_request(rq)
         if name.startswith('book/'):
             name = name.partition('/')[2]
-            if name == '__index__':
+            if name in ('__index__', '__popup__'):
                 send_reply(rq, 'text/html', b'<div>\xa0</div>')
                 return
-            elif name == '__popup__':
-                send_reply(rq, 'text/html', b'<div id="calibre-viewer-footnote-iframe">\xa0</div>')
-                return
             try:
                 data, mime_type = get_data(name)
                 if data is None:
@@ -196,7 +193,7 @@ class UrlSchemeHandler(QWebEngineUrlSchemeHandler):
         if fail_code is None:
             fail_code = QWebEngineUrlRequestJob.Error.UrlNotFound
         rq.fail(fail_code)
-        prints("Blocking FAKE_PROTOCOL request: {}".format(rq.requestUrl().toString()))
+        prints("Blocking FAKE_PROTOCOL request: {} with code: {}".format(rq.requestUrl().toString(), fail_code))
 
 # }}}
 
diff --git a/src/pyj/iframe_comm.pyj b/src/pyj/iframe_comm.pyj
index d8a4d78bd5..851daeb8b9 100644
--- a/src/pyj/iframe_comm.pyj
+++ b/src/pyj/iframe_comm.pyj
@@ -55,7 +55,7 @@ class IframeWrapper:
         self.messenger = Messenger()
         self.iframe_id = ensure_id(iframe, 'content-iframe')
         if ':' in entry_point:
-            self.needs_init = False
+            self.needs_init = iframe.src is not entry_point
             self.srcdoc_created = True
             self.constructor_url = entry_point
             self.entry_point = None
@@ -115,6 +115,8 @@ class IframeWrapper:
         self.encrypted_communications = False
 
     def _send_message(self, action, encrypted, data):
+        if not self.ready:
+            return
         data.action = action
         msg = {'data':data, 'encrypted': encrypted}
         if encrypted:
diff --git a/src/pyj/read_book/iframe.pyj b/src/pyj/read_book/iframe.pyj
index 4954aec0f1..0a23708076 100644
--- a/src/pyj/read_book/iframe.pyj
+++ b/src/pyj/read_book/iframe.pyj
@@ -1006,4 +1006,5 @@ class IframeBoss:
 
 
 def main():
-    main.boss = IframeBoss()
+    if not main.boss:
+        main.boss = IframeBoss()
diff --git a/src/pyj/read_book/view.pyj b/src/pyj/read_book/view.pyj
index f02ac35559..9cf29c06aa 100644
--- a/src/pyj/read_book/view.pyj
+++ b/src/pyj/read_book/view.pyj
@@ -885,12 +885,14 @@ class View:
         is_current_book = self.book and self.book.key == book.key
         self.book_load_started = True
         if not is_current_book:
-            self.iframe_wrapper.reset()
-            self.content_popup_overlay.reset()
+            if self.book:
+                self.iframe_wrapper.reset()
+                self.content_popup_overlay.reset()
             self.loaded_resources = {}
             self.content_popup_overlay.loaded_resources = {}
             self.timers.start_book(book)
             self.search_overlay.clear_caches(book)
+            self.iframe_wrapper.init()
         unkey = username_key(get_interface_data().username)
         self.book = current_book.book = book
         hl = None
diff --git a/src/pyj/viewer-main.pyj b/src/pyj/viewer-main.pyj
index a3f4600088..adeac66e34 100644
--- a/src/pyj/viewer-main.pyj
+++ b/src/pyj/viewer-main.pyj
@@ -442,8 +442,7 @@ if window is window.top:
         , 0)  # We do this after event loop ticks over to avoid catching popstate events that some browsers send on page load
 else:
     # iframe
-    div = document.getElementById('calibre-viewer-footnote-iframe')
-    if div:
-        footnotes_main()
-    else:
+    if document.location.pathname.endsWith('/__index__'):
         iframe_main()
+    elif document.location.pathname.endsWith('/__popup__'):
+        footnotes_main()