Ok, here is the situation.....I have scratch built a model in the Science Fiction genre. The model has various components requiring multiple voltages to operate. 3vdc for the new "noodle LED's", 4.5vdc for an audio circuit, and 9vdc for many of the remaining lights and circuit boards I'm using for effects. The model has a fair amount of cavities to hide wiring, circuit boards as well as batteries. I decided to use two 4000mah 12vdc battery packs constructed from 3 18650 Li ion cells each. The 3 cell size of each pack allows placement in my limited storage areas for two of these packs wired in parallel for a 12.6vdc base source but at the same time I get 8000mah capacity. I have powered one Boost Buck device with the batteries 12v that gives me the 4.5v and the 9v I need. I also powered a smaller Boost Buck device with the batteries 12v to get the 3v I need. Bottom line the power requirements are all met and all systems operate great but here is my question. The packs each came with a small wall wart type charger putting out 12.6vdc @ 1amp (an indicator light is green when plugged in, goes red when charging and goes back to green when the packs 12.6 full charged voltage is reached. (so it says in the instruction sheet) I test loaded and charged each pack before burying them inside my model and they both individually charged fine. As I said I have both packs now connected within the model in parallel to achieve a greater capacity /run time but I kept only one charge jack now that the batteries are in parallel and can be charged together. I operated the model for a demonstration video and then connected one of the chargers to the only jack now connected to the parallel packs and it seems to stay red in charging mode even though over six hours had passed. I have disconnected the charger until I can fathom why it seem the single charger is unable to fully charge the two packs now in parallel. (Maybe the time to charge will take very long, I don't know) Any thoughts? (possibly us a charger of the same 12.6v but with a 2 amp output)?
Thank You

 

Since both Battery-Packs came with a Charger,
and probably have a BMS-Circuit-Board internally,
the best bet would be to install a Double-Pole-Switch that is accessible externally,
and install separate Charging-Jacks, one for each Battery-Pack.
This will facilitate separating the Batteries for Charging,
and automatically connect them in parallel when the Power is turned-On.

An added bonus is that the Battery-Packs will Charge at
roughly the advertised rate of ~4-Hours,
instead of the 8+ hours it would have taken with only one Charger.

To extend Battery-Life, do not store the device with fully Charged-Cells.
Around ~10.8-Volts is a safe storage-Voltage in your case.
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A single charger will take upwards of 9 hours to charge 2 packs in parallel. I wouldn't recommend a higher output charger as there is no paralleling/balancing at the cell level only the pack level so your charger has no way of telling the state of individual cells. I'd go with @LowQCab 's advice and charge separately but don't re-parallel them until both fully charged. As stated, for long term storage (over a month or so), the cells ideally need to be about 70% charged. Simply fully charge both packs, then run for 20 - 30% of normal run time before storing. Store with the packs separated (ie charge mode but no charger connected), then fully recharge both before next use.