Ba'al Hameor and Ravad (both at the end of Pesachim) assume that the communities counted only one day, starting from the first day of Yom Tov. Whether or not they did this with a beracha would probably depend on whether or not you make a bracha on a mitzvah done out of doubt (Rambam to Milah 3:6 says no and the Ravad there argues; Ran Shabbos 23a agrees with the Ravad), though this may be different than the classic case of performing a mitzvah 'just in case'.
The thing is though, even though they remained in doubt for the holidays, the diaspora communities clearly found out at when the right day of rosh chodesh is eventually, because we only have two days of yom tov, and not more (i.e. if they weren't sure when nissan or adar started, they should have 3 days of yom tov). Therefore, by the time Shavuot came around, they always knew when the right day was, and merely kept the second day to be consistent with other holidays (Rambam Hil. Kiddush HaChodesh 3:12).
Therefore, I'm not sure what they did if they found out that they had the wrong day in the middle of sefirah; I assume that they would start counting correctly as soon as they got word that Adar was 29 days. The problem is that the Baal Hameor and Ravad both say that the reason why they wouldn't count two days of Omer is because we don't want to be counting the 49th day of the Omer and celebrating Shavuot at the same time - but (as the Rambam explianed) that should never happen anyway, because by Shavuot there's no reason to count twice!
Therefore, it could very well be that they counted two days (at least until they found out what day it really was). Or, they might have believed, like the Devar Avraham (1:34) that counting two things at once can't really be called a count, and therefore they only counted one day. (The author of the Devar Avraham himself though is hesitant to accept that this is true).
I know this isn't really an answer but it's the best I've got, sorry.