I think it refers to the case of changing JUCE_FORCE_USE_LEGACY_PARAM_IDS between different versions of a released plug-in.
If you release version 1.0 with JUCE_FORCE_USE_LEGACY_PARAM_IDS disabled, and then decide to enable it in a subsequent version 1.1, then it’s very likely that DAW projects created by users with plug-in 1.0 will not load correctly to some extent after they update to 1.1: from automation lanes ending up disconnected, to failing to load their state entirely depending on how the host uses automation to reload it.
But as long as you keep your JUCE_FORCE_USE_LEGACY_PARAM_IDS consistent from the start, then no problems should arise