Unfortunately, the script is simply building upon the built in RoboHelp functionality for popups. If you manually add a Text Only popup, you are going to end up with additional HTML files. One for each popup.
The only real alternative here would be to create a single HTML page with all your glossary terms and definitions, then insert bookmarks at each term and manually create a popup link from each instance to its matching term. Painstaking to be sure, but it's the only way around it that I'm aware of.
Feel free to suggest an enhancement request to see things behave differently in a future release. Click the link below and complete the form to request it.
Thanks for the response. I figured as much but was hoping there was some way around it. We used to have a glossary page with hand-marked terms like you described, but our Online Help is over 1000 topics. It's just not manageable. One of the devs here just created a program that remaps all of the glossary htm files in the WebHelp to global glossary files, so we created a fix that cuts down our file count by around 10,000 files, but it would be nice to not have to do that.
You can modify the script to not create popups in this way but show custom popups or hover text instead. I created something similar for a customer. Let me know if you are interested in exploring the options for this.
For unmarking, a script would be the way I would do it.
While I'd be interested in knowing how you got the script to do that, we've already invested dev time in creating a fix for what we need.
Can you send me a mail on contact [at] wvanweelden [dot] eu? I can send you the code then.
Apologies for the late reply. Just came across this in my inbox again.