I checked a pair of tefillin yesterday where the shel rosh was clearly damaged by a black liquid like substance that had gotten onto the bottom of the shel rosh parshiyos (see pic). After closer examination I saw that the bottom of the bayis, ie the tip of the mechitzos, had it as well (see pic). Clearly liquid entered the bayis at some stage and did damage. I have seen water damage but this was different because it left a grey / black stain whereas watermarks are usually clear. I think what happened here is that the bottom of the bayis had paint which was washed off with laquer thinner. You can still see some of the paint in the charitsim on the underside of the bayis. The dirty liquid (laquer thinner mixed with the paint) went thought the holes of the tefiros and enetered the bayis, staining the lower bayis and the bottom of the parshiyos. Clearly the guy used too much laquer thinner. I cannot think of any other way these parshiyos would have got damaged in such a manner.
The point of this post is two fold:
1) From a halachic / hiddur point of veiw, how bad is the staining on the letters? In the photo the stain looks light but in actual fact it is only a little lighter than the ksav (I think since th ksav being shiny reflected off the flash but the stain being matte did not). In real life you can only make out the tzurah with difficulty.
2) Those who clean the underside of the bayis with laquer thinner should take caution using too much as batim are not waterproof and absorbs liquid much more easily than we think, sometimes with bad consequences!