Replacing original lab-roll media with subtitle-burned versions while preserving existing Merged Clips and sequence references.

1. Name the subtitle-burned versions of the lab-roll files identically to the originals, and save them to a different folder.

2. Rename the folder containing the original media so Premiere Pro can no longer locate it, taking it offline.

3. When prompted to relink, navigate to the new folder containing the subtitle-burned versions.

4. Enable File Name under Match File Properties.

5. Enable Relink Others Automatically.

First of all backup all your files and project files to a different location or storage.

Save another version of your project and work on this new version.

Import your new subtitle-burned versions of your clips.

Lock all your audio tracks.

Use Alt(Option) + Drag from the project panel to the timeline, 

so Alt + Drag each subtitle-burned clip to its corresponding clip on the timeline.

Unlock audio tracks when you finish.

You can also take a look at Automation Blocks if there is any script that

automates this for you, or maybe create your own script that does this, but

always after you backup your project and work on a new version.