When you reconnect the battery, you must lock and unlock the car with the key remote - this initialises the system somehow.
I've never had any immobiliser problems with the safrane however on an older renault we had years ago the flashing would indicate the immobiliser was active. On that car it would crank the engine but not provide ignition - the result being it would turn but not start. I've no idea about the safrane as I've never had the immobiliser give me any hassle.
Did you 'plip' the locking system when you reconnected the battery? - This is VERY important on the safrane. If you did not, disconnect the battery again, reconnect, then lock and unlock as quick as you can. If you don't do this, I think the immobiliser disables the car as it thinks you're not the owner.
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