No. If you change alignments, you immediately lose any "banked" A-Merits.
Spend them before you change. 
Blue
American Steele: 50 BS/Inv
Nightfall: 50 DDD
Sable Slayer: 50 DM/Rgn
Fortune's Shadow: 50 Dark/Psi
WinterStrike: 47 Ice/Dev
Quantum Well: 43 Inv/EM
Twilit Destiny: 43 MA/DA
Red
Shadowslip: 50 DDC
Final Rest: 50 MA/Rgn
Abyssal Frost: 50 Ice/Dark
Golden Ember: 50 SM/FA
Do A-Merits carry over if youre changing from a hero to a villain or visa versa?
@Turbo_Starr