Hi Romain,  Looking at the latest ADF guide as suggested by Michal Keracik there is the option to send custom keys.  On page 2-278 is the command to activate the CTRL key and transmit the combination of CTRL and whatever key you enter next. I have tried this with and other combinations on a DS4308 but it does not appear to work on that model.  So this feature may be scanner specific.

https://atgsupportcentral.motorolasolutions.com/content/emb/docs/manual…

there is "Send Custom Key" action in latest ADF guide that could help

EDIT: Unfortunately it's not working. I've tried it with DS3578 and DS6878 with latest FW on Win8.1 PC.

Easiest would be to create an ADF rule.  Look at the integrator guide of the scanner you are using.