jenkinsci/jenkins — comment on commit a9195825cca348653b7349fa70bd64ec807e7df5
File: core/src/main/java/hudson/init/InitStrategy.java line 58
By abayer:

That sounds reasonable. And it actually sounds quite plausible that you could end up in that situation - the plugin upgrade logic would need to cleanly handle that transition, e.g., and if it didn't (or a plugin was manually uploaded as .jpi after being installed as .hpi, etc), that would need to be handled.