Hello Dishu,
I understand how You build Your system. (Excuse me, i have no
expirience with such type systems, i just coment and my comments can be wrong - with >50% probability).
There is no problem to use this system - with "pipelines"
and complicated software. With some time You will write this software. Other thing , not expalined -how You read 3 sensors
- outputs are shorted and You use 3 output_enable wires for 3 sensors? If so - You again must redesign - to have 3 freqweincies simultaneously readed. And this change can be really big - up to re-layout pcb.
On other hand - such 3-point system has other cons - illumination on 3 points can vary in time, and You have no hardware to recognize this.
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I prefer solution with one point of measurement. Digital output sensors are interesting, but in Your condition You have very critical ratio time_response/time_for_measuremnt.This comes particulary from L/F converter used. For another type sensors(I2C interface) i didnt find time characteristics. So i prefer 1-point measurement, with multicolor sensor with analog output. In this case 3-channel ADC has to be used (Analog device) AD7997,AD7998. If You go this way - You will need NEW small board ,contaning ADC and sensor . Your microprocessor board will be unchanged. Softwware changes will be easier.
regards