Arria 10 aocl flash error

Was that an engineer from Altera or from the board manufacturer? It is highly unlikely that this problem is related to Altera; it seems to be due to defect or bad design of the JTAG controller by the board manufacturers. I have tried two different Arria 10 boards from two different manufacturers and one of them works just fine with 24M clock, while the other one only works with 16M and lower, and in the latter case, the manufacturer also mentions the problem in their user guide. Needless to say, 6M is too low and will significantly increase programming time on Arria 10. I recommend first trying with 16M (which is quite slow as it is) and if it didn't work, going down to 6M.