My answer is D.
A and E are incorrect "they" can refer to small businesses or big businesses.
B is incorrect because of incorret usage of incorrect modifier "formulas".
C is incorrect because of term " same applicability of formulas"

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My 2 cents ..

The term - "because they are growing and are seldom in equilibrium" is clearly referring to "small businesses" therefore it must be touching it. In the original sentence it can easily be confused with big businesses i.e. big businesses are growing and are seldom in equilibrium.

Therefore A is wrong ..

B - Because they are growing and are seldom in equilibrium, formulas for cash flow and the ratio of debt to equity do not apply to new small businesses in the same way as they do to established big businesses.

B is suggesting that the formulas for cash flow are growing and are seldom in equilibrium. This is clearly not what the sentence is trying to imply ... (common sense) ...

B is incorrect ..

C - Because they are growing and are seldom in equilibrium, new small businesses are not subject to the same applicability of formulas for cash flow and the ratio of debt to equity as established big businesses.

Clearly the mistake which dogged the statement A and B has been rectified here .. So C can be shortlisted ...

D - Because new small businesses are growing and are seldom in equilibrium, formulas for cash flow and the ratio of debt to equity do not apply to them in the same way as to established big businesses.

The same mistake that dogged A and B is now corrected in D , therefore we can shortlist it as a potential correct answer.

E - New small businesses are not subject to the applicability of formulas for cash flow and the ratio of debt to equity in the same way as established big businesses, because they are growing and are seldom in equilibrium.

This passage again suggests that established big businesses are growing and seldom in equilibrium .. Therefore it is WRONG ..

We are down to 2 potentially correct choices C & D ...

Out of the two , I think that D delivers the message (that the author of the passage wants to deliver) better, and in a more simplistic form than C . There may well be a grammatical reason for why C is not correct but i have not been able to pin point it. I base my answer on simplicity and clarity..
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Ans E because in the others ans they or them can refer to small businesses or formulas