You want the origin and destination fixed effects to vary by year. So, the right way to include the fixed effects is
Code:
ppmlhdfe FDIflow lnvreer lnreer lngdp_o lngdp_d lngdpcap_o lngdpcap_d, absorb(isonum_o##year isonum_d##year pair_id) cluster(pair_id)
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