Describe the bug
First reported over xJon/The-1.12.2-Pack#990, I can reproduce the issue with all of the versions of AE2 Unofficial Extended Edition I tested.
Changing to the normal (old) edition (rv6-stable-7) resolves the issue.
I am unable to reproduce the issue with just AE2 Unofficial Extended Edition installed, so I guess it is an incompatibility with one of the mods in The 1.12.2 Pack, but I was unable to figure out which one.

To Reproduce
In The 1.12.2 Pack, since version 1.5.0 a couple of years ago when it changed to AE2 Unofficial Extended Edition:

1. Setup an auto-crafting process for a Fluix Seed, and an auto-smelting process for a Pure Fluix Crystal.
2. Request a Pure Fluix Crystal - it should work
3. Restart the game fully, and try again to request a Pure Fluix Crystal - it should not work, showing this:
   
   And requiring you to re-create the Fluix Seed auto-crafting Encoded Pattern.
   If alternatively you want to auto-craft Fluix Seeds directly (rather than through the Pure Fluix Crustal process), there is no issue:
   

Any input would be appreciated!

Upon further testing, it seems that manually inputting the items in the Pattern Terminal - and not utilising the HEI auto-fill - prevents this issue from happening. Strange... I guess it is not an AE2 issue directly, then?

The same issue occurs, and I have a video reproducing the problem - https://www.youtube.com/watch?v=EXlpAJgxAws. The modpack is Infinity Evolved: Reloaded. All patterns were manually created using crafted items. The issue is described further here for the modpack author:
"At certain crafting stages, the ME system freezes. Similar to the issue with the BatBox in the video, I also encountered this while crafting circuits (a problem with copper cable). When ordering a BatBox, Tin Cables disappear in the system, causing freezes and disruptions in earlier crafting stages. Additionally, rubber couldn’t be retrieved (a previous issue, but this time without opening the recipe through HEI—removing the Storage Cell helped). After a "reload," 3 Tin Cables appeared, which were created during the first attempt. The earlier stages became accessible, but now the system doesn’t recognize Tin Cables for the BatBox crafting."

I created a new issue here - /issues/525