The current version of stacking used in the abilities system is one of the newest parts of the system. As a result you’re more likely to encounter rough edges and bugs here.
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Unfortunately, yes what you’re describing is currently impossible to implement in a straightforward manner. I can think of a couple really hacky ways to set up your data that would work but I won’t discuss them since I don’t want to encourage those approaches. What you described seems like a very reasonable thing to want to do in the system. We’ll need to figure out the best way to support it.
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Looking at your first screenshot everything looks ok. My best guess here is something weird going on with the stacking rules. As I said earlier this is the area most likely to have rough edges. When I’ve got a bit more time I’ll try to reproduce the problem. Unfortunately this is a busy time of year so it could take me a couple weeks to get to it.
The behaviour you described for your second screenshot is expected. Effects with an instant duration make permanent changes to the attribute values. You can think of periodic effects as a way to repeatedly execute instant effects. The modifiers aren’t outliving the effect, the actual attribute value has changed.