That question doesn't have one cut and dry answer.
1) Replace them when they are bad, or missing. A lot of folks buy project games, and have to piece them together. Some older games have chip legs that tarnish, and if you pull the chip, the legs can break off. Any time there is physical damage, or a ROM is missing, you need a replacement
2) Replace them when the game is in the wrong language, most DE/Sega/Stern games were exported, and when they were brought back in, they were in the wrong language
3) Replace them when features are added, or bugs are fixed - WMS started keeping logs of changes around ST:TNG - games before then don't really have a list of what the ROM revisions changed - so it's a guessing game in most cases.
4) Replace them just because you want to - I have customers who insist on new ROMS in any game they purchase. That's a bit excessive IMO, but I'm not going to turn the business away.
Hypothetical example: Customer asks me what changed between Pinbot L-4 and L-5? I don't know. It could be something major, or a European distributor could've complained that something was spelled wrong, so they fixed it and released an updated ROM. US customer buys replacement Pinbot ROMS, installs them, and finds no difference. Well, that's because the change is in the German part of the ROM, and you won't notice unless you change the game to German. The same applies to diagnostics or audits. Perhaps there was a misspelling, or a test that you will likely never use could've had a bug fixed, etc.