HTML 5 converstion

First, I'll just say that I'd avoid any manual manipulation of a file in post. Especially if you have a large number of courses you're maintaining - or if the company might at some point hire another person (or you get hired by someone else), another person has to know which courses have post-publish-modified code and remember to make X change each time they publish Y file and follow Z process to get it to work. 

That said, I'm not sure what you're trying to gain (i.e. don't have the software anymore and can't publish, save time, etc. If you don't have the software anymore (and can't republish), then that's sort of its own sticky situation you'll have to work around-- this may be it...would still make me all "itchy" though for potential future issues knowing how things evolve and change.

I don't know much about the LMS you are using, so I'm not sure how you'd modify just one file (seems you'd have to re-version the course anyway and at that point) but I'd probably just republish html5 only and get a clean package on the server.  

The reason is who knows if the admin will run a search on courses post-December and either remove/archive files with .swf or send an email to the course owner to tell them there are .swfs in the course and that they need to be removed.

The other concern I might have is if Storyline's naming convention changes. For example they used to have a story_html5.html, but now it's gone. For the situation it seems you are describing (modifying a file in post) this probably wouldn't be an issue (if you republish, you'll overwrite the file you manipulated), however if you used some sort of server-level redirect (i.e. IF launch = index_lms.html redirect to story_html5.html), you could run into a whole host of issues.

I'm also not sure if you're publishing AICC or SCORM, but publishing in newer version of SL fixes the Chrome 80 change in how data transfer is handled (impacted AICC) - so it might be that you should republish anyway.

Just food for thought :)