I have fixed this particular issue, but I noticed a lot of | conditions in the default actions of statuseffects.txt (eg. Ham-Fisted default action is "use 1 jug of hamethyst juice|use 1 flask of hamethyst juice|use 1 vial of hamethyst juice"). I don't know if someone either thought these would work, planned on adding | to the CLI interpreter but didn't or simply left them there as a place-holder.
I went ahead and retroactively fixed other occurrences of | in the database. For item using in the CLI, it's simple enough to do "use either 1 x, 1 y, 1 z" so I did that where possible. There are a few things (such as recordings) that needed to be handled using an ash one-liner. Not fully tested, as I don't have all these items/skills.