Hello ,
Can you share the LACP config from SRX end . It may be possible that you have some LACP fast setting and while pushing the configuration the RE CPU might have spiked hight and caused the LACP PDUs to miss and caused the flapp ( as you said the physical interfaces where UP ) . This is just an assumption . This can be confirmed only after a detailed analysis of logs from SRX . So if you are looking for an RCA , I hope its goot to open a JTAC ticket to investigate further on this .