The procedure you’re describing is the correct one for loading old pipelines. However, remember CellProfiler is not intelligent enough to adjust all downstream modules to incorporate the changes in your parameters. For example, if you fix your RescaleIntensity module because it has changed in this new version, remember that all downstream modules have to be re-told the name of your rescaled image- otherwise they will fill in the default. If you forgot this, that could be why even after saving and reopening, it appeared as if some modules had reset (ie, SaveImages might show RescaledBlue, despite the fact that your rescaled image is named something else, and you already changed and saved this!).
I would double check this first, because typically adjusting the parameters, saving, and reopening is the correct procedure. If that doesn’t work, something else might be going on.
Let me know!