For the LimeSDR you can get the modified gateware from that answer above.
You need to use the GPIO pin 0. When it’s low, the timestamps returned by the Lime are normal, but when it’s high the timestamp stops changing and it’s high bit becomes 1 (if you use SoapySDR, the timestamp will be negative). Once you put it low again, the timestamps continue as if nothing ever happened (so you don’t lose track of time).
So to synchronize your 2 devices, you would put both GPIO[0] low, then high at the same time, then back low. At first both devices will have normal timestamps, then at one point the high bit of the timestamp will become 1. The first timestamp for each device with a high bit of 1 correspond to the same time.