That is unclear. I would believe that the Reapers would be completely destroyed, unlike the derelict which still had a functioning core, and therefore could still slowly indoctrinate. Thunder
Reapers are indeed completely destroyed in Destroy ending and in Synthesis, indoctrination is not needed anymore. Land Raider
^ But I got the impression Reapers can't choose not to indoctrinate. If they keep doing it even after death... Will-O-Wisp
^ The "Destroy" wave fired by the Crucible apparently tore apart the very essence of the Reapers, that's the way I interpret it. They're nothing more than mountains of junk now. Land Raider
The Reapers ‘die’ in Destroy, so I suppose their ability to indoctrinate is lost (in that, they indoctrinate via infra/ultra-sonic sound waves, so them ceasing to function would mean such sound waves would cease to transmit). In Synthesis, everything understands everything else---you can see the husk that was attacking the Alliance soldier ‘wake up’ after being hit by the wave---so the Reapers and their ‘offspring’ (husks, cannibals, brutes, etc.) are now friends with the things they were previously trying to kill.
- That's actually only part of the method they use for indoctrination- the full process is never completely explained (and if sonics were the only thing they were using, shielding against it would be easy enough that no one who was aware of the effect would be at risk of it). 6thLyranGuard
- The Codex also cites electromagnetic fields, but again, any generators of those would shut down when the Reaper does. Sound is also not restricted to affecting your ears (you feel bass more than hear it, for example), as it is a wave that bombards everything it comes into contact with. The only reason it is related to sound is because the ear is sensitive enough to differentiate between high and low pitches, different tones, etc. (the same as the eye are able to differentiate between short and long wave-lengths of light). In the case of sonics, I always considered the Reapers were in constant motion---vibrating constantly, but in so minute or subtle a manner as to not be detectable to anything coming into contact with them (allowing for the Derelict Reaper mission in ME2).