Currently the armor refinement amalgamator is severely bugged.
In the following examples I'll refer to the refinements as either Refinement A, or Refinement B to make my examples more clear.
If you have 2 of the same armor refinements in your inventory (ex. Gloss of Hardening - Woodland Armor) and you use the Armor refinement amalgamator on Refinement A, but instead of clicking Refinement B you click on Refinement A again it consumes Refinement A but does not give you an upgraded refinement.
When upgrading armor refinements with the amalgamator it should work the following way:
2 refinements of defense = 1 refinement of protection
3 refinements of protection = 1 refinement of hardening
4 refinements of hardening = 1 refinement of fortification
5 refinements of fortification = 1 refinement of invulnerability.
currently it works as:
2 refinements of defense = 1 refinement of protection
2 refinements of protection = 1 refinement of hardening
2 refinements of hardening = 1 refinement of fortification
2 refinements of fortification = 1 refinement of invulnerability.
Certain armor refinements are allowing you to pick more mods than they should for the level of refinement being used.
example:
Fortification level enhancements should only have you select 3 mods as the bonus mod would random if successful (4th resist). Invulnerability level allows you to pick 4 and if the bonus mod is successful it's the (5th resist).
In the following examples I'll refer to the refinements as either Refinement A, or Refinement B to make my examples more clear.
If you have 2 of the same armor refinements in your inventory (ex. Gloss of Hardening - Woodland Armor) and you use the Armor refinement amalgamator on Refinement A, but instead of clicking Refinement B you click on Refinement A again it consumes Refinement A but does not give you an upgraded refinement.
When upgrading armor refinements with the amalgamator it should work the following way:
2 refinements of defense = 1 refinement of protection
3 refinements of protection = 1 refinement of hardening
4 refinements of hardening = 1 refinement of fortification
5 refinements of fortification = 1 refinement of invulnerability.
currently it works as:
2 refinements of defense = 1 refinement of protection
2 refinements of protection = 1 refinement of hardening
2 refinements of hardening = 1 refinement of fortification
2 refinements of fortification = 1 refinement of invulnerability.
Certain armor refinements are allowing you to pick more mods than they should for the level of refinement being used.
example:

Fortification level enhancements should only have you select 3 mods as the bonus mod would random if successful (4th resist). Invulnerability level allows you to pick 4 and if the bonus mod is successful it's the (5th resist).