Hi
I think you are using the Time alarm interrupt as the wake up source.
This is intterrupt is gennerated when 【LPSRTCMR + LPSRTCLR】bit[46:15] = TA.
Besides this, this counter is a up counter. So that, if you didn't clear the LPSRTCMR and LPSRTCLR, the interrupt will no be generated becasuse 【LPSRTCMR + LPSRTCLR】bit[46:15] is bigger than TA.
So that, i think your can using the following code as a reference:
unit64_t time = (SNVS->LPSRTCMR)<<32 + SNVS->LPSRTCLR;
time = time / 32k;
SNVS->LPTAR = time + your new wake up time in second.
Please have a try.