I'm playing ATM10-Sky. Please do let me know if you think this bug report belongs at the pack. However, it strikes me as a direct mod issue.

I've been taking advantage, perhaps unwisely? of my ability to directly link chests and barrels within the controller's range, rather than using a Storage Link. I have an array of barrels and sieves near a controller, but not adjacent, linked with the tool. When I hold the tool, I can see that they're linked, and everything usually works as intended.

However, that controller is hooked up, via Integrated Dynamics, to a Functional Storage controller (sorry, different needs, different solutions) and to a Productive Metalworks foundry. It exports ores to the foundry, and anything the drawer system contains goes to the drawer system. Most of the time, this works as intended.

However, every few hours of playtime - it's SSP - I notice that my sieves' output barrels are not themselves outputting to the other systems. When this happens, I get the tool, re-link the barrels to the controller, and everything starts working again. I have discovered that I don't even have to unlink them first; I get the tool in linking mode, I right click a misbehaving barrel, and it starts behaving again.

I will definitely need more info to be able to recreate and fix. Based on what you're saying it seems like it happens in the same play session and you're not exiting world / loading it again, correct? Are you going far away / changing dimension so that chunks could potentially unload? Are the chunks chunk loaded?
This info likely won't be enough to recreate but may help to point out what could be causing an issue.

I'll need to pay more attention to the surrounding circumstances for a day or two to be sure. Will update.