The key charges as you drive. If you use the remote alot but drive lots of short trips, it may not have enough time to charge. Is that a possiblilty?
Read these tech notes:
Vehicles affected: E36, E38, E39, E46, E52, E53, E83, and E85 with electronic immobiliser 3 (EWS 3)
Cause
If the key is not removed from the ignition lock completely (semi-removed status), there is a critical distance between the key and the ring antenna where the EWS will detect statuses permanently changing between "key inserted" and "key removed". This will result in a permanent closed circuit current of approximately 800 mA.
Measure
In the event of a complaint, explain to customer that he should either leave the key fully in the ignition lock, or remove the key from the ignition lock completely.
Parts replacement does not provide a remedy
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Complaint
The customer complains that the remote key does not lock/unlock the vehicle - the battery in the remote control is discharged
Vehicles affected – all models 2000MY-on E38, E39, E46, E52, E53, E60, E65, E66, E85.
Cause
1) Battery needs recharging
2) Key is defective
Measure
Analysis of remote control keys returned in warranty show that many are not defective. Only the battery needs to be recharged. Note that without use, the battery will only retain its charge for approximately 1 year. The Owners Manual advises that the key must be used at least once per year (driving for an extended period) to maintain its state of charge.
In case of complaint, check with the vehicle owner if the problem key is the key regularly used, or the spare key.
If the spare key is the problem, and a short drive puts sufficient charge in the battery to make it operational again, do not replace the key, but explain to the customer that the key must be used occasionally (driving for an extended period) to maintain its charge.
If the regular key is the problem, replace the key.
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Battery Charging
The new key transmitter does not use regular batteries but rather a rechargeable vanadium*lithium* storage battery. New radio transmitters will be supplied with charged storage batteries.
*Important: Always dispose of keys according to state/local laws.
In ignition lock position 1 (terminal "R"), the storage battery is charged inductively. The charging process is realized via the ring antenna of the ignition lock and via the coiled antenna integrated in the radio transmitter. An electronic charging unit in the key controls the charging process.
The battery is designed for a very long service life. The key must be used to prevent discharge .
If the keys are not used, the storage battery is discharged after 18 months. With completely discharged storage batteries, the full charging period will be approx. 30 hours (to maximum battery charge).
After charging for 30 minutes, the remote control can be actuated approximately 15 times.
Key voltage monitoring
If low voltage of the key has been reached, the central locking system can no longer be locked using the remote control. The "convenient opening" can no longer be used, nor can the radio transmitter be initialized.
Each time a key button is actuated, the storage battery voltage in the key is monitored. Once the "low key battery" signal is contained in three consecutive key transmissions, it is stored together with the corresponding radio transmitter key number for diagnostic purposes in the general module. The low voltage entry is automatically deleted when five consecutive key transmissions no longer contain the "low key battery" signal.
Otherwise, the dealer is basically correct - "No user replaceable parts inside" so to speak.