I see that people have suggested this post correction equation ((b1 le 0)*0+(b1 ge 10000)*1+(b1 gt 0 and b1 lt 10000)*float(b1)/10000) for atmospheric correction using FLAASH (where surface reflectance values are not within the normal range. Just curious to know if there is any reference to back this up in case one wants to publish such result in a journal.
Having to limit the reflectance to range between 0 and 1, by using a formula like that, is very indicative of your atmospheric correction being incorrect. If it is something that occurs often, you should consider using a different method, where you have better control over the parameters, such as 6S.
As for a reference for limiting the range of reflectance values, the physical meaning of 'reflectance' means that no values outside that range can exist, and therefor, implementing a 'capping formula' should have no impact. If you are doing a applied paper, that should be enough (potentially with a remark towards edge effects on imagery etc), if you are doing a theoretical paper, then the fact that FLAASH causes results like that should be more of a worry for you causing you to go for a more robust approach to atmospheric correction.