Multiple sequence setdowns being called in PremierePro

I'm using the AfterEffects SDK to create a plugin for both AfterEffects and PremierePro.
I save the project data in sequence_data.
When the project reopens, the data is loaded back from the sequence_data. This works fine for AfterEffects, but in case of PremierePro, sequence_setdown is called multiple times, and flatten is not call before the project closes.

However, if I set this flag, PF_OutFlag2_PPRO_DO_NOT_CLONE_SEQUENCE_DATA_FOR_RENDER, then it works fine for PremierePro as well. All the sequence_data is coordinated properly then. But the SDK advises against setting this flag. Also, my renders get slower if I use this flag