You do not need collapse or "problematic things" to describe non-linear processes like spontaneous parametric down-conversion. The OP's observation that the scattering matrix in quantum field theory is a linear operator on Hilbert space does not prohibit non-linear processes in the quantum optical sense.
The point is that you have to ask the question "linear in what?". Processes such as spontaneouus parametric down-conversion are typically non-linear in some observable, but can be obtained as completely normal unitary evolutions of the wavefunction (see also my answer here).
To illustrate this, consider a two-level atom coupled to a single electromagnetic field mode (i.e. the Jaynes-Cummings model). It constitutes a pretty standard quantum theory with the interaction Hamiltonian
$$H_I = g(\hat{a}\hat\sigma^+ + \hat{a}^\dagger\hat\sigma^-) \,.$$
So the wavefunction will evolve in the usual linear way. However you will find that the operator equations of motion are non-linear in some sense, e.g.
$$ \frac{d}{dt}\hat{\sigma}^- \propto \hat{a}\hat{\sigma}^z \,.$$
If you look at this from the perspective of correlation functions, you can construct the BBGKY-Hierarchy for these equations. That is, if you take into account an infinite hierarchy of correlation functions, the equations remain linear. However, it is also easy to see how non-linear optical processes occur in this system. As an example, for the case of many photons, mean-field theory is often applicable, such that we can approximate
$$ \langle\hat{a}\hat{\sigma}^z\rangle \approx \langle\hat{a}\rangle\langle\hat{\sigma}^z\rangle \,.$$
The resultinig semi-classical equation of motion is then manifestly non-linear due to the product between two operator expectation values and this is precisely what results in the non-linear optical response of this system.
For spontaneous parametric down-conversion, the concept applies identically, but the underlying model is more complicated, which is why I chose a simpler example above.
With regards to the edit of the question, which seems to be about the black hole information paradox, I will just point to this recent popular article, which summarizes recent work proposing a solution within semi-classical quantum gravity. While still under debate, this seems to follow a similar principle: the dynamics of a simple quantum + gravity model lead to complex dynamics of the information flow.