I came up with a workaround for anyone still having this issue! Since the issue comes from the full deck achievement i just removed it from the achievements list, launched the game and attached with the correct shifted units.

Steps:

goto (steam directory) \SteamApps\common\Endless Legend\Public\Statistics and Achievements

open file AchievementDefinitions.xml 

Delete all the acievements in the last section (then end of file should look as follows:)

[...]

    <!-- Winter Shifters -->
    <AchievementDefinition Name="COLLECT_ORBS_PLAYTHROUGH" />
    <AchievementDefinition Name="COLLECT_ORBS_OVERALL" />
    <AchievementDefinition Name="COLLECT_BIG_ORB" />
    <AchievementDefinition Name="FIGHT_ON_ICE" />
    <AchievementDefinition Name="DROWN_ON_ICE" />
    <AchievementDefinition Name="CAST_VOTES_OVERALL" />
    <AchievementDefinition Name="ALL_ORB_UNLOCKS" />
    <AchievementDefinition Name="FORCE_SHIFT_OVERALL" />
    <AchievementDefinition Name="BATTLE_SHIFT_FORM_VARIETY" />
    <AchievementDefinition Name="MANTA_EXTRACTION_OVERALL" />

</Datatable>

Complete the acievement it will unlock.

Of course now your install is corrupt so you have to do a verify integrity of local files on steam to fix the file if you did not save a backup copy.