Even though we do not have this extra 'vav' in our Sifrei Torah, and even though the Minchas Shai who was a contemporary of the Ramban states that he has never seen a Sefer Torah with this extra 'vav', nevertheless, the fact is not only did Rashi have it, but also the Ibn Ezra and the Chizkuni. Therefore, it would be useful to try and understand why the 'vav' logically should be there according to their Sifrei Torah.
First let us look at the posuk again with the taamei mikra - the cantillation notes.
וְנֽוֹעַדְתִּ֣י לְךָ֮ שָׁם֒ וְדִבַּרְתִּ֨י אִתְּךָ֜ מֵעַ֣ל הַכַּפֹּ֗רֶת מִבֵּין֙ שְׁנֵ֣י הַכְּרֻבִ֔ים אֲשֶׁ֖ר עַל־אֲר֣וֹן הָֽעֵדֻ֑ת אֵ֣ת כָּל־אֲשֶׁ֧ר אֲצַוֶּ֛ה אֽוֹתְךָ֖ אֶל־בְּנֵ֥י יִשְׂרָאֵֽל
Note that under the word העדת there is a note which looks like an upside down Y. This is called an esnachta, and it indicates a pause in the middle of the posuk (all or nearly all the posukim of the Torah have such a note in the middle), something like a semi-colon that we use in our sentences. Because of this pause, the two parts of the posuk need to make independent sense, and in our posuk if there is no 'vav' the second part of the posuk says "all that I will command you unto the Children of Israel", which makes no sense by itself.
But Rashi and the Ibn Ezra deal with this 'vav' in different ways.
The Ibn Ezra understands the first part of the posuk "I will arrange My meetings with you there, and I will speak with you from atop the ark cover from between the two cherubim that are upon the Ark of the Testimony" to mean that Hashem will communicate privately with Moshe, teaching him secrets and answering his questions, and he explains that the phrase "I will speak" also applies to the second half of the posuk: "and (I will speak) all that I will command you unto the Children of Israel". Hence we see how according to the Ibn Ezra the second half of the posuk makes sense with the 'vav'. (The Chizkuni understands the posuk in a similar fashion).
But Rashi deals with the 'vav' by calling it superfluous and subservient and thus ignores it, since he understands that the simple explanation of the posuk is to read the complete posuk as one statement, that Hashem is communicating to Moshe only that which he is to tell the Children of Israel. But since the posuk in reality has a 'vav' there is also a different, deeper understanding of the posuk, reading it in two halves. (Possibly Rashi thinks that the explanation of the Ibn Ezra (or something similar) that Hashem also communicates there secrets to Moshe, is the deeper understanding).
In conclusion I should point out that in practical terms it makes no difference whether in fact the Torah is supposed to have a 'vav' there or not, since Chazal have already told us that we are not expert in all the 'vavs' in the Torah, and thus the Torah is valid either way.