It was replaced by Arabic as the majority in the 11th Century (or at least reached parity), and was oft persecuted against by the Mamelukes in various forms from the 13th Century onwards (with the first big anti-Copt riots in 1259). The big date where the change was complete was in 1354, where the normal anti-Christian policies against the Copts were expanded to include even those Copts who claimed to have converted or were (possibly) only nominally Muslim. Accusations abounded that they were crypto-Christians and essentially almost all of their waqf lands were confiscated and their churches burned. Since then, Egypt has pretty much retained the 90%/10% ratio it currently has.
This is interesting, I must have misinterpreted whatI had read. Certainly, though, the Coptic language was still being spoken in the 17th century, and it is worth noting that, at least outside the capital, Coptic still held a fairly prominent position for at least half of the CK2 timeframe. It is of significance that the Egyptian culture in the game is shown as being Islamicized but still using Coptic names.
The importance of Coptic in religious life cannot be underplayed either, as the language of liturgy, if still spoken, often makes killing of said language as a native tongue a long and brutal process. For example, while many say that Hebrew died as a spoken language in Alexandrian times or even earlier, giving way to Aramaic, we have a lot of evidence to support its survival into the 4th century of the Common Era. Aramaic had use, certainly, we see loanwords into Hebrew (bar-), an Aramaic-origin script in use, and Aramaic names coming from Judea, but they held stubbornly to their language and became bilingual in the lingua franca and the local tongue instead of wholesale abandoning the Hebrew language despite government working in Greek and Latin as trade worked in Aramaic.
I can say that during the 9th century, Coptic was still the language spoken by near all of Egypt beyond the capital. It was Pope Gabriel II who would first introduce Arabic into the Egyptian liturgy in the 12th century. I have also read that the Fatimids, apart from Caliph al-Hakim, were quite tolerant and led the Copts to relatively flourish. As far as I've read, the big era of persecution and conversion was more the 14th-15th centuries. There's also to be considered the contrast between urban populations (which by the start of the 20th century were ~15%, recorded as ~6% by the 1950s) and rural populations. Until somewhat recently, like much of the world, the majority of the population lie in rural regions.
I know Severus ibn al-Muqaffa wrote in Arabic, and stated his concern about his fellow Copts speaking it, and I will admit here that I am not extensively familiar with this man, but would it be unreasonable to assume he is speaking of a more local issue? After all, the 10th century was
hardly the end of Coptic language, we are quite sure of that. There are texts that we know in Arabic but once likely held Coptic language versions as well, ironically some lamenting the loss of Coptic to Arabic. The Apocalypse of Samuel is one example, though it has been dated anywhere from
the same century as Islam was birthed, an extremely unlikely option to be losing Coptic given that this was a period of intense resistance with a vast Christian majority, while some of the text itself indicates a setting during the Crusades.
Bohairic Coptic is still considered spoken widely enough by the 14th century that Copts are still writing their bibles in it, though they have bilingual versions in Arabic as well dating to the 12th century. Though, some from this era (12th-14th centuries) are also bilingual in Coptic and Greek instead of Arabic. The shift from Sahidic to Bohairic is also quite significant, as it would indicate (at least to me) that the language was prevalent enough still to care about the dialect used and, indeed, to actually have another dialect to switch to at all. Of further note, while many texts are bilingual in Arabic and Coptic throughout the Mamluk era, there are still monolingual biblical texts being produced as late as the 16th century. In a time near the end of the Mamluk rule, when restrictions and riots weren't as bad, and when the Ottomans came knocking and actually took over the place, a monolingual Coptic language translation of a biblical book is produced.
Honestly, I'd say that if Coptic were truly dying that fast, then there might be more priests complaining about it, but all I can find are those two. Severus and a text we can't even properly date or assign authorship. That seems to be it. I can't find with ease any hard figures concerning the ratio of Christians to Muslims throughout the Middle Ages, but we have evidence to suggest that there were many Muslim converts who continued to speak Coptic- namely due to all the persecutions and paranoia surrounding them.
While there was an ongoing shift during this whole period, it is difficult to determine when precisely it dropped out of majority. The presence of bilingual texts seems to me to indicate that, in some part, there was still a group large enough to warrant it. When you go back to being monolingual, it means either that it is dead and the text is only for priests to read, or that there is still a following that the translation is meant for. Their general flourishing at times as well would tell me it didn't see much decline during said times. Lastly, Egypt is one of the first places to seem to have built up an actual nationalism, based on modern concepts of ethnicity, and to this very day they will stand adamantly and deny being Arab. Considering the long period of conflict throughout the Early Middle Ages, I think it is safe to say that they would not be loosing their identity too fast.