There are two problems in this passage. First, in verse 27 the 1837 edition inserted the indefinite quantifier many before churches in the yea-clause, probably because of the immediately preceding “there were many churches in the land”. This change could well be accidental. It is definitely not necessary for the sense. Since both the 1830 edition and the printer’s manuscript lack the many in the yea-clause, most probably the original manuscript also lacked it. It is possible, of course, that the determiner many was lost while writing down Joseph Smith’s dictation. Nonetheless, given that the yea-clause does not need the many, the earliest text (“yea there were churches”) will be restored in the critical text.
The other problem in this passage is the textual switch from the plural churches in verse 27 to the singular church at the beginning of verse 28 (“and this church did multiply exceedingly”). In verse 27 the text quite clearly is referring to more than one church (even if many is not included in the yea-clause). This shift from plural churches to singular church appears to have been original to the text. The singular usage in verse 28 (“this church”) is supported by the singular in verse 29 (“and again there was another church”). One could possibly emend verse 27 in the yea-clause by having “yea there was a church”, but then the use of the yea-clause would seem strange since the preceding clause definitely refers to “many churches”.
Don Brugger points out (personal communication) another possible way to interpret the difference between churches and church in this passage. The initial “many churches” in verse 27 could refer to various congregations (or churches, in the plural) that all belonged to the same sect (or church, in the singular), thus “this church” in verse 28. There is definitely evidence in the Book of Mormon text for such usage, as in Mosiah 25:22: “and thus notwithstanding there being many churches they were all one church / yea even the church of God”. (See under Alma 8:23 for a complete discussion of the two distinct meanings in the Book of Mormon text of the word church.) In other words, the two instances of church in 4 Nephi 1:28–29 may refer to different sects, while churches in verse 27 may refer to different congregations of the same sect. Yet even with this interpretation for 4 Nephi 1:27–29, the shift does strike one as odd, especially since there is no explanation as in Mosiah 25:22 for the shift in grammatical number. In any event, the shift here in 4 Nephi 1:27–29 does appear to be intended and the critical text will retain it.
Summary: Remove the intrusive many in the yea-clause in 4 Nephi 1:27, giving “yea there were churches which professed to know the Christ”; the unexpected shift from plural churches in verse 27 to singular church in verses 28–29 appears to be original to the text and will be retained.