This comes up every so often, but as this is a new forum, there's no prior report here.
There is currently no mechanism for taking things out of containers apart from processing the contents (e.g. eating it) or moving it to another container. Emptying a container means pouring the contents on the ground, which means it's lost when liquid or fine grained. The logic doesn't contain any exception for items that can exist as free items, so they're lost as well.
It can be noted that this is a general container issue, not a mod one, as you can do the same with vanilla containers such as bowls or pots.