A few months ago I saw M. Pinchas' post about Havchanat Tinok in regards to Shem Hashem. He was confronted with the following problematic Yud from "Elokim" :
The Yud is too long and it resembles a Vav, causing a paradox: if it's a Vav, this is a clean-cut Psul in the Sefer Torah and it must be fixed. However, if it's a Yud, it's forbidden to touch it since the word is already Holy (Elokim is one of Gd's names) and warrants no fix. In other words, both options are quite dramatic - a potential psul vs. the issur of fixing a proper Shem Hashem.
M. Pinchas, based in the Or Hamelech, invoked the Havchanat Tinok solution to figure out which way to go. It has been some 4 months since I read this but it stayed in my mind since then, as this is a quite puzzling and delicate situation.
Last week I saw in the Ot Yatziv from Zanz (a great new sefer on Stam) a discussion about this and he concludes that in the case of Shem Hashem we should consider this letter to be a Yud, even though it's too long, because according to many opinions even a long Yud is still a Yud if it has a "Kefifa", curve, and I think the Yud of Elokim seen above has a slight kefifa.
According to this view, the Elokim should be considered kasher and therefore holy, and shouldn't be fixed. See the text below:
The author goes on to explain that many Sofrim write a long Yud purportedly, because of Kabalistic motives, and that there's no reason to render them Pasul.