No, regular merits are not affected by alignment shifts in any way. 
Loth 50 Fire/Rad Controller [1392 Badges] [300 non-AE Souvenirs]
Ryver 50 Ele� Blaster [1392 Badges]
Silandra 50 Peacebringer [1138 Badges] [No Redside Badges]
--{=====> Virtue ♀
Thank you!
Make a man a fire and keep him warm for the day, SET a man on fire and keep him warm for the rest of his life.
Incarnates: K'lir(Fire/Dark Corr):Hot-House Flower(Plant/Fire Dom):Kinrad X(Kin/Rad Def):Itsy-Bitsy Spider(Crab):Two Ton Tony(Mace/WP Broot):Teeny Weeny Widow(Fortunata/Widow) : Zeroth Law (Ice/Fire Tank)
I know I can gain an A-Merit for confirming my alignment.
I know I lose A-Merits if I switch sides.
If my hero decides to switch side (first vigilante, then villain), do I lose regular merits? My gut says no, but I was hoping someone may be able to confirm?
Make a man a fire and keep him warm for the day, SET a man on fire and keep him warm for the rest of his life.
Incarnates: K'lir(Fire/Dark Corr):Hot-House Flower(Plant/Fire Dom):Kinrad X(Kin/Rad Def):Itsy-Bitsy Spider(Crab):Two Ton Tony(Mace/WP Broot):Teeny Weeny Widow(Fortunata/Widow) : Zeroth Law (Ice/Fire Tank)