If youre missing a Phylake on the map go to the region
on the map where the Phylake usually is and light one the braziers
in any of the camps and the Phylake will go to it.

Lake Mareotis - The Outsider (Level 20)
Sap-Meh Nome - Ptolemy's Fist (Level 22)
Ineb-Hedget Nome - The Iron Ram (Level 24)
Memphis - The Stranger (Level 28)
Faiyum - Ra's Mercy (Level 30)
Faiyum Oasis - The Hill (Level 32)
Haueris Nome - Bane of Hathor (Level 35)
Im-Khent Nome - Half Horn (Level 38)
Isolated Desert - The Galatian (Level 40)
Isolated Desert - The Iron Bull (Level 40)

PS: If you forgot which one of them is missing you probably have to go trough all of them to find the remaining Phylake to kill.
If you forgot to confirm their deaths i think they will respawn in their specific areas again but you won´t see any icons on the map.
I hope this guide helped to fix your problem and i´m sorry if it didn´t work for you!