After deconstructing my Kovarex processing plant, the Fabricator now has a lot of U-235 and even more U-238 which can't be removed or used.

It also stored 250k wood after I removed trees within my roboport coverage.

Your Mod portal description notes its possible to remove these items later, but I can't see anything that would allow this

This behavior isn't obvious or optimal, but there aren't many good solutions to this problem. The mod already prioritizes placing unusuable items to the player's inventory, I thought about making leftovers to just spill around the player but decided it would be even worse that sending them to the limbo.

In the next update there will be a way to manually remove any items from the storage. The mod wasn't intended to be some sort of global linked storage, so the way to automatically remove items via Dedigitizing reactors is intentionally slow and locked behind Aquilo tech.