To edit content in a scrolling frame, you could resize the frame to reveal the scrollable content and edit it there.
It sounds like your embedded content method may have had issues with the links from the embedded content to the document in which it was embedded. Here's some information on relative links that can help:
It's possible that you might have more luck making the glossary a second document that you export separately and then embed into your main document using the in5 Web Content interactive widget. The embedded document can scroll and have text anchors.
If you make links from one document to another (from the glossary document to the main text document), then I would recommend making relative links to the pages. Here's how to make relative links:
Link from one document to another with InDesign and in5
If you want to link to a specific page in the main document and it was exported with the Output set to Web, then use the following syntax in the URL where this example would take you to page 2:
Link from outside to a specific page of a long document