I think you misunderstood. There was no compatibility problem with the probe ship files, but the active ones in a save still had stock fuel and I needed to finish up with them first.
Yes, scaling down the engine caused negative mass. It happened to all engines connected to real fuels (KSPIE engines worked fine, as did non-engine parts). Later, I removed all mods except Tweakscale, Real Fuels (stockalike configs) and their requirements, and the problem persisted. I vaguely remember encountering this before, and I've found it mentioned on a few other posts.