Tosafos explains that when the gemara says that store owners in mechuza who are only in the store by day, not at night, can make a chazaka, means that after they spend 6 years in the store to make up the time of the missing nights in the first 3 years, they have a chazaka. Tosafos equates this with the gemara that says that a field that is left barren every other year, requires 6 years to make a chazaka. Being that the stores in mechuza are no different than the fields that are worked every other year, Tosafos is bothered what is the chiddush of the stores in mechuza? Tosafos answers that since there are many stores that are set up in peoples homes so that they are in fact there both day and night, one may have thought that it is not possible to have a chazaka by just being there by day only. The gemara is mechadesh that after 6 years their would be a chazaka. But, by an olive press and fields that no one ever uses at night, Tosafos admits that 3 years is sufficient to create a chazaka. The requirement of making up the nights only applies to areas that some people use both by day and by night.
However, the Rashbam seems to disagree with Tosafos. In the context of the field that is left barren every other year, the Rashbam writes that the barren year does not count toward the years of chazaka and must be made up. But in the context of the stores of mechuza, the rashbam writes that even without living there at night, it is a fine chazaka since these stores are only meant to be used by day. What is the difference? In the case of the barren field also we are speaking about a place where it is normal to leave every year barren, so what is the difference?
The simplest distinction is that when he is there for all 3 years just that he is missing some time within the year, he doesn't need to make it up, but if he is missing the entire year then he must make it up.
But, perhaps we can offer a different distinction. In the case of the field that is left barren, the fact that it is normal in that place to leave the fields barren only compensates for the claim of לא אחזיק כדמחזקי אינשי. This is very meduyak in the Rashbam that the fact that it is normal to leave it empty is considered - כדמחזקי אינשי, and therefore isn't regarded as a hefsek in his chazaka. However, the field is able to be used every single year. It may not produce as much if used every year, but since it can be used every year, the machzik is expected to be there every year. When the owner notices that no one is there for the middle year, he assumes that no one is trying to make a chazaka and has no reason to protest - so there isn't a chazaka until 6 years pass. But, in the case of the stores where it is normal to be used by day, not at night, the time of night does not need to be made up because the machzik is not expected to be there at night. Based on this distinction, it doesn't matter whether the time that is missing is short (such as a night) or long (such as a year), the real difference is only whether the machzik is expected to be there during that time so that when the owner claims that he didn't protest because he noticed that the machzik was absent, he has a valid ta'nah.