If you use touphscript to edit the text, you may be able to completely avoid any conflicts with the hardcore mod. No file replaces are necessary. Look into it.
If you are altering script (as in game programming script NOT text), then flevel would still need the files replacing, but seems to me you aren't doing that? As long as your mod was installed first and hardcore mod doesnt alter any of the aerith files, your mod would be cool. Even if it did, you could always include a modified harcore text version for the specific flevel files.
touphscript does not need to replace files, it uses text files that you can edit then ship with installer at encode time. It alters ALL the text in the game (inc the kernels, scene, ff7.exe, world map) and will auto correct scene lookup table in kernel.
It also ignores any lines in non dialogue files that are blank.