The מחבר (סימן תפ”ט סעיף ז’) says that if one forgot to count sefirah at night, he should count by day without a brocha. The reason for this halacha is that many poskim are of the opinion that בדיעבד sefirah by day is a good sefirah. However a brocha is not said because we must take into consideration the opposing view that sefirah is only by night. He may continue to count with a brocha for the rest of sefirah. The reason explained in theשער הציון that it is a ספק ספיקא לחיובא. The first ספק is if one can count בדיעבד during the day. The second ספק is if every night is a separate mitzvah or they are all one continuous mitzvah. If it is one long mitzvah one may not continue to count because it is no longer תמימות – complete. If they are all separate mitzvos then he may continue to count with a brocha. According to this opinion תמימות has a different meaning [look at ביאור הלכה ד”ה סופר בשאר ימים]. Even if counting during the day is not good even בדיעבד, still maybe each night is its own mitzvah. Therefore he may continue to count the rest of the nights with a brocha.
The מחבר in the following halacha (סעיף ח’) says that if one was unsure if he counted sefirah the previous night and he also did not count by day, he may continue to count the rest of the nights with a brocha. Here too well it is because of a ספק ספיקא. The first ספק is that maybe he did count. The second ספק is that even if he did not count maybe the halacha is like the poskim that every night is a different mitzvah. He may therefore continue to count with a brocha. The Mishna Berurah adds that this applies anytime he is counting because of a ספק. For example if you only counted days and not weeks or the other way around, it is a מחלוקת if it is a good counting. He may continue to count the following nights with a brocha because this is also a ,ספק ספיקא since there is always theספק if it is one mitzvah or separate mitzvos.
The מחבר in the beginning of סעיף ח’ says that if one forgot to count the sefirah he may not continue to count with a brocha The reason is we must take into consideration the opinion that sefirah is one mitzvah. What is the halacha if one remembered the following day during בין השמשות? For example he forgot to count the fifth night and right before the sixth night he remembered that he did not count. The time he remembered was בין השמשות. This time period is a ספק if it is day or night. Since we are only dealing with one ספק he should count without a brocha.
What about the following nights – may he continue to count with a brocha? Reb Shlomo Zalman zt”l is of the opinion that he may not. The Mishna Berurah explained the reason one may continue to count with a brocha is because of ספק ספיקא as explained before. Since we have two ספיקות telling us that maybe he fulfilled his mitzvah he may continue to count with a brocha. In the case of בין השמשות however, we have a ספק ספיקא לחומרא going against us. We can never say for certain that he counted during the day for we always have the ספק that maybe it was the night. We can therefore not say that the first ספק is if counting by day is good because we don’t even know for sure that he counted by day, maybe he counted by night. We only have one ספק maybe every night is a separate mitzvah. One may not count with a brocha on the צד of one ספק. Reb Shmuel Wosner zt”l disagrees and holds that even in this case one may continue to count with a brocha. Since at the end of the day there are two reasons to allow him to continue counting with a brocha since maybe his counting was by day and maybe every night is a different mitzvah.
Prepared by R’ Avrohom Yehoshua Ziskind
 Sources:משנה ברורה,ביאור הלכה,שער הציון,דרשו