Dear Alexandru,

That should be happening in drivers/iio/industrialio-buffer.c in the
iio_enable_buffers() function.
The channels get enabled by writing via sysfs in
/sys/bus/iiio/devices/iio:deviceX/scan_elements  in the _en files.

libiio typically does this manipulation of files for you

I thought so too and I can confirm that when I switch back to less 
channels that the others are disabled. However the scanmask is not updated.

See some logging here trying to debug:

Session 1, read 8 channels:

iio_readdev -b 262144 -s 1024 iio:device0 voltage0 voltage1 voltage2 
voltage3 voltage4 voltage5 voltage6 voltage7 > /mnt/test6.bin
8 active channels
[  513.529510] acq_buffer_preenable
[  513.529521] active scan mask: 0x000000FF
[  513.558286] acq_buffer_postenable
[  513.716868] acq_buffer_predisable

Session 2, read 16 channels:

iio_readdev -b 262144 -s 1024 iio:device0 voltage0 voltage1 voltage2 
voltage3 voltage4 voltage5 voltage6 voltage7 voltage8 voltage9 voltage10 
voltage11 voltage12 voltage13 voltage14 voltage15 > /mnt/test6.bin
16 active channels
[  523.834056] acq_buffer_preenable
[  523.834067] active scan mask: 0x0000FFFF
[  523.880440] acq_buffer_postenable
[  524.041383] acq_buffer_predisable


Session3 ,  read 8 channels again:

iio_readdev -b 262144 -s 1024 iio:device0 voltage0 voltage1 voltage2 
voltage3 voltage4 voltage5 voltage6 voltage7 > /mnt/test6.bin
8 active channels
[  532.002019] acq_buffer_preenable
[  532.002030] active scan mask: 0x0000FFFF
[  532.048375] onr_acq_buffer_postenable
[  532.131081] onr_acq_buffer_predisable

so, are you using an Analog Devices kernel?
or is this a vanilla mainline kernel? and which version?
ADI has some custom patches that deal with this some scanmask manipulation;
is this being reproduced purely with libiio? and which version of libiio?
steps to reproduce?

i'm still not sure if the issue is in kernel or in libiio;

Yes I am using a adi 4.14 kernel, git tag adi-4.14.0  15e1a16477

For iio_readdev I am currently using the v0.21 zerocopy checkout

Henk