Does the aluminium chloride assay (Ordonez et al.2006) for total flavonoid content work on coloured extracts?
Depending on the intensity of the yellow color (specifically, the degree of absorption of light at the wavelength of your measurement) you might be able to subtract out the yellow from the extraction in order to differentiate between that and the color arising from the aluminium chloride assay.  

In other words, just measure the absorbance of your material before the addition of your reagents, and subtract that value from your final absorbance reading.  

Alternatively, since this is a matrix interference issue, you might do well using the method of standard additions. This is described in this Wikipedia article:  


  The method of standard addition is a type of quantitative analysis approach often used in analytical chemistry whereby the standard is added directly to the aliquots of analyzed sample. This method is used in situations where sample matrix also contributes to the analytical signal, a situation known as the matrix effect, thus making it impossible to compare the analytical signal between sample and standard using the traditional calibration curve approach.  


This article gives a reasonable outline of the procedure that should be sufficient should you decide to try this method.