Well. Manually I mean not using time clock with pool for on and off auto mode. Reason is that RJ board (my current ) does not use safety flow switch.
Correct, the RJ model does not use a flow switch. The RJ mainboard is a crippled version of the HP (US version).
So when pump stops on auto it keeps making chlorine in none moving water. Hence the safety issue.
I think you got this wrong! On the Aquatrol RJ (US version), only the power LED stays ON and the in-house timer runs for as long as the AC power is present. When the timer is set to ON (auto or manually), the pump runs and the "No Flow" LED blinks for a few seconds and goes Off. If no error is detected, the "Generating" LED will come on and the cell produces chlorine.
When the timer reaches the preset OFF position, the pump stops and the "Generating" LED goes off, indicating that the power to the cell is disconnected. Hence, the chlorine production is suspended. Again, only the "Power" LED will remain lit for as long as the AC power is present. If your RJ bd does not function as I described then yes, you have safety issues.
Please observe your RJ and confirm the sequence of operation.
So how did you swap data between the EEPROMs? From my research the AQR, HP, RJ PCB are same. Only difference is the programming data. My end game is to get the HP version working in my box unit. Is there a way to save the EEPROM data and put in a file or usb stick? Tht would be helpful to mod boards.
The Aquarite is designed for the in-ground pools while the RJ and HP models are for above-ground. Re-flashing the sw and re-programming the EEPROM is a risky business and requires some soldering skills to remove the EEPROM from the pcb. I can provide a walkthrough but so you know, you are on your own on this. Yes, the sw.hex and EEPROM.bin can be extracted from a known good source and transported through a media like a USB stick.
Anyway, you are not limited to a costly HP replacement bd. If I were in your shoes, I'd rather get a pre-owned Aquarite bd r1.59 for less than $100. The Aquarite bd offers more flexibility and fits the Aquatrol box without mods. Let us know how you want to proceed.
Btw, you haven't posted the diagnostics. Would you know the software revision? Not sure why the seller says the first box is faulty unless it's an old rev. Just curious!