1. Even Rav agrees that there are cases of a Shomer being for an item that is less than the size of a bean.
2. The Gemara quotes a Mishnah that discusses the many different Halachic statuses of onion peels.
3. The Gemara proves from this Mishnah that a Shomer that is on top of a Shomer does not have the status of a Shomer.
4. Regarding Tefilin there is a law that there may not be any holes in any of the letters in the parchment.
5. A hole that ink passes over is not considered a hole regarding Tefilin.
A BIT MORE
1. It is clear that the peel of a lentil is a Shomer, despite the fact that a lentil is less than the size of a bean. This is because it is an entire entity that was created less than the size of a bean, as opposed to the peel on half of a lentil that is not a Shomer.
2. For example, the innermost peel of an onion is considered food and, therefore, can become Tamei along with the food. The middle peel is considered a Shomer if it does not have holes.
3. The last part of the Mishnah states that the outer peel of an onion is not a Shomer, as it is a Shomer that is on top of a Shomer (the middle peel).
4. This would render the letter invalid (depending on where exactly the hole is in the letter).
5. Accordingly, if there is a miniscule hole in Tefilin parchment, but the letter that it is in does not seem to have a hole in it, the letter is valid.