Abstract: The invention discloses a method and an apparatus for in-line and on-site updating of Field Programmable Gate Arrays with remote loaded configuration data files. Flash EEPROMs which are used because of their non-volatile memories and their high density, are storing more than one configuration data file. The memories are divided in more than one part, each part of the memory for storing one configuration data file. One part of the memory also contains a flag identifying the currently loaded configuration data file. The Flash EPROM's bits being set to one same binary value before any writing operation, including the update of the configuration data file containing the flag. The setting of the bits to said binary value always identifies a valid other configuration data file in order to insure a correct re-loading of the FPGAs in case of reception of an unexpected event leading to an initialization.