There is an issue in the mod version 2.0.5 (the one currently used in the modpack) described in #282 (which was not resolved) that makes it impossible for the Seed Reprocessor and the Soul Extractor to receive input seeds/soul material, making it impossible to automate these devices. This was fixed in version 2.0.6 (see patchnotes for https://www.curseforge.com/minecraft/mc-mods/mystical-agriculture-refabricated/files/4599590), but the modpack never updated to that version, and thus the bug is still present, which is quite a big issue.
On a quick glance I did not see where the versions of the mods are defined in this repo, otherwise I would have made a pull request, so I'm making this issue instead.
I realize the modpack kinda outlived itself at this point and work is focused on AOF7 probably, but it would be a shame to leave the modpack in this bugged state when the solution is so simple.

Do you know what version it was initially upgraded to? Which mod was it conflicting with? Was it ever reported to its github repository?https://github.com/AlexSa1000/MysticalAgriculture-Refabricated

2.0.8 though during troubleshooting 2.0.6 was tried. Conflicted with patchouli I believe. Caused crashing in spectrum due to patchouli multiblock visualizations

Because of that bug, I added an MI counterpart that does the exact same thing. (not the soul extractor though). If you really really want to automate it, and are partially into MI (electric age) you can use that if you'd like!

the pack updated to a later version but that caused crashes with other mods so the pack had to downgrade the MA version again. MA has not been udated to prevent causing crashes in other mods, so it cant be updated to fix the issues you describe

Unfortunately I really dislike MI, and I imagine other players don't want to get into it either, so it would be nice to have both devices working properly.

In my own AOF6-based modpack, with Mystical Agriculture: Refabricated v2.0.8, Patchouli v1.19.2-77-FABRIC, and Spectrum v1.6.12-1.19.2, multiblock visualizations appear to be working fine. I tested displaying Spectrum's "Pedestal CMY Upgrade" and "Enchanter", as well as building the former using Patchouli's hologram. Maybe the issue has been fixed since then?

If someone could find proper reproduction steps for the bug it would be very helpful. We could then test the issue on the current build + updated Agriculture 2.0.8 and see if it's still present.

DaFuqs/Spectrum#209

It was an issue in 1.6.11. There were several dependency updates and guidebook changes in 1.6.12, so it could be that it works now, though i would suggest testing it by interacting with the guidebook, and each of the structures (both built and incomplete) with the proper advancements

Unfortunately, most recently, with Spectrum v1.6.12 + Mystical Agriculture: Refabricated v2.0.8, Spectrum's guide book ("Colorful World") failed to load properly (through Patchouli), stating that the "spectrum:fusion_shrine_structure" multiblock could not be found. Downgrading Mystical Agriculture to v2.0.5 resolved the issue, and I haven't looked too closely into it since...

Unfortunately, most recently, with Spectrum v1.6.12 + Mystical Agriculture: Refabricated v2.0.8, Spectrum's guide book ("Colorful World") failed to load properly (through Patchouli), stating that the "spectrum:fusion_shrine_structure" multiblock could not be found. Downgrading Mystical Agriculture to v2.0.5 resolved the issue, and I haven't looked too closely into it since...

When was that?

I believe I have found the issue.

Mystical Agriculture depends on code in one of its libraries, "Cucumber", to access the client's RecipeManager.
However, in the Fabric port of Cucumber, the relevant code is never initialized, thus causing an error during resource reload, and eventually preventing Spectrum from loading the assets for its (data-driven) Patchouli book.

I was able to fix this by forking Cucumber and implementing a ClientModInitializer that listens to the appropriate event(s) to initialize the aforementioned code. I'm not sure whether 1.19.2 is still supported by Cucumber / Mystical Agriculture, but I suppose I'll make a PR anyway.

(pinging @AlexSa1000)