Hmm, never had any problems with polys, beside the fact that Altium handles them very clunkily. You can (usually?) route traces over a polygon as if it's not there, and repour as needed (always remembering to repour before generating fab files! argh!). In my flow, I only shelve to get the damn things out of the way (visual clutter, and also moving things around, layout and routing).
If you have overlapping polys, one will pour over the other and the overlapping area can be indeterminate. To fix this, repour all, and set the pour order in the Manager (T, G, M). Or just try to avoid overlapping polys. I find this most useful when placing polys on a layer with a ground pour; the smaller polys need to pour first, otherwise the ground poly fills in and nothing works.
I don't see any reason one should be handling polys by lucky saves and moving junk around. That sounds fantastically fragile. It is literally my business

to address or prevent situations with unwanted memory, hysteresis, undefined quantities and so on. Polys can be one such example, and approaching them in a way that prevents these unwanted aspects is the best approach.
Tim