I noticed that the upgrades are missing in JEI for @YABBA, so I checked the logs for errors relating to YABBA and I found a bunch of warnings along the lines of:

[19:46:37] [Client thread/WARN] [minecraft/ModelBlock]: Unable to resolve texture due to upward reference: #tex in yabba:models/item/upgrade_base

It also seems that each of those warnings is always followed by an error along the lines of:

[19:47:10] [Client thread/ERROR] [FML]: Could not load override model thermalfoundation:item/tool/fishing_rod_stone_cast for model thermalfoundation:models/item/tool/fishing_rod_stone

So is there some kind of conflict between Thermal Expansion and YABBA?

If not then how come I don't see the upgrades, I wonder?

This is basically FTB Ultimate Reloaded, 1.12.2 (inc. their configs) with a few additions and removals.

If you need any more information then just let me know.