It is normal to charge lead-acid batteries in series. As they are used, the cell voltages will change, which is why they are not charged in parallel. If they were charged in parallel, the one with the high voltage wouldn't get much current, and the one with the low voltage would get too much current.
With the cells in series, they all get the same amount of current, and all get approximately the same amount of charge. Since they will not charge and discharge exactly the same, the battery voltage and level of charge will gradually drift apart.
To handle this, it is common to periodically do an "equalization" charge, where you overcharge the string slightly to bring up the charge of the undercharged cells. You do this because lead-acid batteries handle overcharge better than they handle undercharge.
You have done that, and at least one of the cells has gassed. Check the fluid level, and next time charge to a slightly lower voltage. Only do equalization every couple of months. If some of the cells fail, it will not be possible to charge the battery fully. When that happens, it is time to throw out the battery.
This is one of those best-practices arguments that never actually gets a really good answer. There is nothing technically wrong with having that light-green jumper installed. But the problems start when you begin to consider the failure modes of the batteries.
As lead acid battery ages, its internal resistance increases as things build up on the plates, and the plates themselves begin to break down and change shape. Eventually, the plates will fail, and you will probably wind up with a shorted cell in one of those batteries. If it goes open (which is rare), all is well and you just lose the capacity in that set - but you have to consider the short as the most dangerous possibility.
When this happens, if that jumper is installed, the half of the batteries on the same side as the faulted pack are going to discharge through the dead battery with virtually no resistance. This can be an incredibly bad thing, potentially resulting in a catastrophic discharge, and possibly exploding cells.
With the jumper out, you still have the entire bank of batteries discharging itself, but it would be reduced by the internal resistance AND voltage of the other battery in the line that didn't short out. Any resistance is better than no resistance, and the voltage reduces it even further, so the battery pack you are worried about protecting is actually needed to prevent a potentially devastating current flow.
Of course, it is worth pointing out that what you have done is technically no worse than paralleling any number of single battery packs. But the internal short problem is the primary design consideration that makes almost every battery bank go in series first, and then add banks in parallel - it helps that those lead acid batteries themselves are a number of cells in series, packaged as a single unit.
So, from a best practices perspective, you really should remove that jumper. Any compromises made to protect equipment, in this case, merely endanger other equipment in a different way, and create new concerns about your safety.
Best Answer
This sounds like a bad idea. Besides the fact that it says not to do this on the battery package, here is the reason:
simulate this circuit – Schematic created using CircuitLab
As you can see, the batteries that are used have a lower cell voltage, but also a higher internal resistance. They aren't contributing much to the power delivery, and they will dissipate quite a lot in heat! This will eventually rupture the battery.
Your bypass might work if the circuit is capable of using a lower voltage, and the batteries you use are capable of delivering a higher current to compensate for the reduced voltage.