Question

Its safe to delete .prd files and non prd files which was stored under C:\Program Files\FlexNet Operations\release\flexnet-data\data\prd folder

Answer

Yes, its safe to delete all the files under C:\Program Files\FlexNet Operations\release\flexnet-data\data\prd folder unless if we don't want for diagnostic/debugging perpus (better to keep last 30days files)

The name of the PRD file will be <activationId>-<system timestamp>.prd and The name of the command file will be <activationId>-<system timestamp> ( without any extension ).

For example:

Worth reading more information about prd files and how to disable prd files then click here