Those were done with the original ROM layout. Temporal Flux doesn't work within the shared text banks, it gives each event packet its own little text block. If other tools don't analyze the event packets, they won't know the new text locations and will fail to get the new text.
It's not what it's meant for, and it wouldn't let you reinsert the text, but you could use the "translation project" feature on a copy of the ROM and then examine the "Translation.Project" file in a hex editor.