Generating two secret keys from a physical analog signal: Crypto HASH analogous to time varying signal
There seem to be multiple problems you try and solve at once. Lets split the problem in at least two sub-problems:


First of all you want to have to extract entropy;
Then you want to create two keys using the entropy or random number generator.


Extracting the entropy

Extracting the entropy from the source involves whitening techniques. In case the amount of entropy is low you may want to use this entropy as input to a DRBG (deterministic random bit generator).

You may also want to include other entropy sources or identifiers, anything that may add randomness if you're using a DRBG.

Lets call the resulting bit string with $K_{master}$. $K_{master}$ does not have to be formatted as a key, it's just a bunch of bits that together hold a minimum amount of entropy.

Creating two separate keys

OK, so now you need two separate keys that are independent on each other. This is easier then you may think; you can simply use a KBKDF such as HKDF, which is based on a hash function: $K_1 = \operatorname{KBKDF}(K_{master}, \text{"1"}, l)$ and $K_2 = \operatorname{KBKDF}(K_{master}, \text{"2"}, l)$ (where $l$ is the amount of bits required for $K_1$ and $K_2$.

HKDF first explicitly extracts ("compresses") the entropy in the key to a fixed size output that depends on the hash algorithm used. It then expands this extracted information into enough key material for $K_1$ and $K_2$. Of course the strength is limited by the entropy in the input key material and the used hash function (however SHA-256 or higher should be enough for any normal usage).

You could include a device specific secret into the IKM by appending or prefixing it to the $K_{master}$ that you got from whitening your entropy source.

Most importantly, revealing either $K_1$ or $K_2$ to an attacker won't give the attacker any information on the other key or the input keying material (given it has enough entropy not to be brute forced).



This way you can focus on the best way to get entropy from your source. Try not to create any data that depend on other data as you seem to suggest.