This scenario will, as stated, trigger the 60% rule at the beginning of the spring semester of his 4th year in college (14.4.3.2.3). It isn't clear however that he will actually have met the requirement that he "shall have completed successfully at least 60 percent of the course requirements in the student’s specific degree program. ...... The course requirements must be in the student’s specific degree program (as opposed to the student’s major).
Can the JC offer courses in his third year that are transferrable to the second 4 year school and are acceptable to his "specific degree program"? Plenty of college students start their 4th year of full time enrollment, have scads of credit hours, but are behind in taking the specific courses needed for their particular degree program. One way for this to happen is to change degree programs, but another way is spend a 3rd year at a JC, since JCs typically doesn't offer courses suitable for the third year of a degree program. I suppose that 4 year schools vary in the amount of flexibility given to students in choosing courses, so it probably depends on his second 4 year school.
One other thing, and I recommend checking with the NCAA about it. D1 baseball has special rules, and 14.4.3.2.3.1 says "Exception—Baseball. In baseball, a student-athlete who is ineligible under this provision at the beginning of an institution’s fall term shall not be eligible during the remainder of the academic year." Additionally, there is also a 40% rule for players entering their 3rd year, and I guess he'll be subject to it when he enters the second 4 year school. You'll want to make sure that he can meet the 40% requirement. I don't think this will be an issue, but he should check.