I suspect that what you have estimated from your retrospective data is "prevalence," not "incidence." This distinction is explained for example in this paper. "Incidence" is the rate at which a condition occurs, for example the fraction of a population that develops the condition per year. The fraction of people that currently has the condition, whenever it first occurred, is "prevalence." Although it might be possible to use retrospective data to examine incidence, if you simply collect retrospective data on a set of patients and determine the fraction of them that had the condition, you are examining prevalence not incidence.
What follows, however, is the same regardless of whether you are examining incidence or prevalence.
The paper cited above points out that:
... all epidemiological studies are (or should be) based on a particular population (the ‘source population’) followed over a particular period of time (the ‘risk period’).
Your estimate of sample size thus needs to based on the "source population" from which you are sampling. In retrospective clinical data analysis you are "sampling" (typically, taking all cases) from the population that happens to have shown up for clinical care and thus is included in the data set. If that group of patients is your source population then you should use the characteristics of those patients as your guide to study design.*
The problem you face, as noted in a comment on your question, is extrapolation to the general population. You cite a 100-fold difference in "incidence" between the population from which you are sampling and the general population. That would seem to be a potentially serious problem.**
So if you wish to make any statements about the general population rather than just the "source population" that underlies your retrospective data, you must take the difference between the populations into account. As the above paper notes on page 395:
... some prevalence studies may involve sampling on exposure status, just as some incidence studies may involve such sampling. For example, in a study of a group of factory workers, asthma prevalence may be measured in all exposed workers and a sample of non-exposed workers. This sampling scheme does not change the basic study type, rather it redefines the population that is being studied (from the entire group of workers in the factory to the newly defined subgroup).
You might think about your situation as over-sampling the disease cases, similar to what's described in the preceding quote. But for the results to be interpretable in terms of the general population, you would have to document that both the disease cases and the non-disease cases in your "source population" are representative of what's in the general population. Given the apparently large difference in prevalence/incidence that you note and my experience with analysis of retrospective clinical data, my guess is that the characteristics of the non-disease cases in your data will a good deal different from the general population and that you will have to take that difference into account in your study.
*In single-institution retrospective analysis, trying to get a larger sample size generally means going back farther in time for more cases. Among other things, you then need to see whether there have been changes over time in incidence/prevalence or in the characteristics/risk factors of the retrospective-patient "source population."
**Some of the magnitude of this discrepancy might be due to a difference between incidence and prevalence, for example if this is a long-term condition and the value of 0.1% for the general population that you cite is truly an incidence rate (say per 100,000 people per year) and the 10% value you have estimated from your retrospective data is prevalence. Nevertheless, there would still seem to be some difference between your "source population" and the general population.