Sorry clio should have picked that up from your original posting.
The forced ventilation system will have been designed as a system and will probably be rendered ineffective if you leave doors open, the HSE advice is much to simplistic for your situation. A DSEAR assessment must surely have been carried out in the past to justify the installation of the ventilation?
You are right about signage and controls and permit to work will be needed to control activites if it is a potentially hazardous area. Battery charging area signs are too general- the signs should identify the hazards and controls required- eg yellow graphic hazard of corrosive liguids, red no unauthorised persons, green eyewash station, blue eye protection must be worn etc.
There is no reason why the system should not be left running overnight if it has been properly designed.
The procedure is that the DSEAR assessment will cover the process risk of charging the batteries, and all necessary measures to avoid fire or explosion arising from the process. The outcome of the DSEAR assessment will allow fire risk assessment of high, normal or low risk as appropriate and the necessary fire related issuies- rate of growth, enclosure, travel distances, alarm and detection, etc will follow from this.