I seem to be frequently running into an issue on a server I'm using where adding items to a filter module will not acknowledge those items and allow them to be passed into the attached containers mid game. I have to restart the server for it to update, this is time consuming and not overly practical to do regularly so I was wondering if there is a command to refresh filters or reload the plugin without having to completely restart the server.

Cannot reproduce this issue. Please try to reproduce it with just Pretty Pipes installed.

I'll try, the problem is it doesn't happen when the server first boots up. I'm not sure if it's a time issue or something like when I move away and come back it stops working. Will have to do some more testing I guess as it's super weird.
Any time I add a brand new filter and add items it'll work, but then after that if I try to add new items to the filter it just wont register those new items when dumping them into the system.
If I can figure out what triggers it I'll get back to you.

I can confirm this Problem. When the Server is running for a while newly added or modified filters & prio modules wont be recognized. I can't however reproduce this behavior in single player with the same modpack. Even breaking and replacing the pipe does not help. However after a restart everything works as intended again.

Please send the full server log of a session where this happened, as well as the full client log of a client experiencing these issues.