There’s at least two effects to consider. First, the acid/base treatment is likely to denature proteins and disrupt membrane integrity. Second, chloroform extraction will separate the lipids from the membrane leaving the proteins behind. But transmembrane proteins generally have very hydrophobic trans- or inter-membrane regions, so that once the lipids have been extracted, the membrane proteins tend to aggregate, as their hydrophobic regions try to exclude solvent by associating with other hydrophobic regions on anything that happens to be nearby. This usually doesn’t do the protein structure much good, either. So the net effect of chloroform is to at least aggregate, if not denature, membrane proteins as it solubilizes the membrane lipids. This effect is probably independent of any acid/base effects – more or less independent, anyway.

Sorry, three factors to consider: the freeze-thaw will also denature some proteins. It’s not clear to me how the experiment was designed, so I can’t say much more.