Hi! I'm not the nominator, but very familiar with this fandom, and Fire Emblem Series is definitely an overly general fandom tag that shouldn't be used for exchange purposes. It's like MCU, Final Fantasy Series, Dragon Age, etc---the games are completely separate in all practical terms.

Here are the ship tags in question and the AO3-approved names of the fandoms they should be under:

Alm/Clea | Clair (Fire Emblem) - Fire Emblem Echoes: Mou Hitori no Eiyuu Ou | Fire Emblem Echoes: Shadows of Valentia
Asama | Azama/My Unit | Kamui | Corrin (Fire Emblem) - Fire Emblem: If | Fire Emblem: Fates
Berkut/Rinea (Fire Emblem) - Fire Emblem Echoes: Mou Hitori no Eiyuu Ou | Fire Emblem Echoes: Shadows of Valentia
Chrom/Tiamo | Cordelia (Fire Emblem) - Fire Emblem: Kakusei | Fire Emblem: Awakening
Dyute | Delthea/Ryuto | Luthier (Fire Emblem) - Fire Emblem Echoes: Mou Hitori no Eiyuu Ou | Fire Emblem Echoes: Shadows of Valentia
Ephraim/Heanius | Innes (Fire Emblem) - Fire Emblem: The Sacred Stones
Frederick/Liz | Lissa (Fire Emblem) - Fire Emblem: Kakusei | Fire Emblem: Awakening
Gangrel/My Unit | Reflet | Robin (Fire Emblem) - Fire Emblem: Kakusei | Fire Emblem: Awakening
Hinata/Oboro/Takumi (Fire Emblem) - Fire Emblem: If | Fire Emblem: Fates
Ike/Senerio | Soren (Fire Emblem) - Fire Emblem: Soen no Kiseki/Akatsuki no Megami | Fire Emblem Path of Radiance/Radiant Dawn
Leanne/Naesala (Fire Emblem) - Fire Emblem: Soen no Kiseki/Akatsuki no Megami | Fire Emblem Path of Radiance/Radiant Dawn
Lukas/Robin | Tobin (Fire Emblem) - Fire Emblem Echoes: Mou Hitori no Eiyuu Ou | Fire Emblem Echoes: Shadows of Valentia
Makalov/Marcia (Fire Emblem) - Fire Emblem: Soen no Kiseki/Akatsuki no Megami | Fire Emblem Path of Radiance/Radiant Dawn
Makalov/Stella | Astrid (Fire Emblem) - Fire Emblem: Soen no Kiseki/Akatsuki no Megami | Fire Emblem Path of Radiance/Radiant Dawn
Maribelle/Wyck | Vaike (Fire Emblem) - Fire Emblem: Kakusei | Fire Emblem: Awakening
Marx | Xander/My Unit | Kamui | Corrin (Fire Emblem) - Fire Emblem: If | Fire Emblem: Fates
My Unit | Kamui | Corrin/Takumi (Fire Emblem) - Fire Emblem: If | Fire Emblem: Fates
My Unit | Reflet | Robin/Walhart (Fire Emblem) - Fire Emblem: Kakusei | Fire Emblem: Awakening
Reyson/Tibarn (Fire Emblem) - Fire Emblem: Soen no Kiseki/Akatsuki no Megami | Fire Emblem Path of Radiance/Radiant Dawn
Senerio | Soren/Skrimir (Fire Emblem) - Fire Emblem: Soen no Kiseki/Akatsuki no Megami | Fire Emblem Path of Radiance/Radiant Dawn