Inductive Charging 2 layer coil transfer to 1 layer receiver. Any issues?
will I be able to increase my magnetic field strength and thus increase efficiency?


Yes, magnetic field strength will be increase if you keep same currents in the coils. However, increased field strength does not guarantee higher efficiency. For the purpose of maximum efficiency you should look for kQ product as follows - This assumes your load is at its optimal value.
$$\eta = k^2Q_1Q_2/(1+\sqrt(1+k^2Q_1Q_2))$$
$$k = M/\sqrt(L_1L_2), Q = \omega L/R$$
Having multiple layers in Tx side will increase the self inductance(L_1) mutual inductance (M) and  - in most cases, coupling will also increases. However, AC resistance of Tx will also increases with the increase of number of turns. Therefore, your quality factor may be affected. You should carefully examine how the quality factor varies. 
Usually, if your operating frequency is not very high and coupling coefficient is very small, adding an extra layer helps to improve the efficiency. 


  What are risks associated with this mismatch?


Having different Tx and Rx coils does not mean low performance. If you carefully redesign the system with modified parameters, you can get the best out of it. without actual specifications such as power level, coils size, distance, frequency etc, it is hard to say how to optimize and what will happen.