What are the consequences of jumping a broken FL11 next to the battery

There is no FL11 in an iPhone SE, I believe you are referring to FL2400. Here is what the SE looks like.

The picture you provided is an iPhone 5S and you are not highlighting the proper part. Here is the 5S battery connector layout and FL11 highlighted in yellow.

Regardless, they both serve the same purpose. This component is a chip ferrite bead and it is used to filter high frequency power supply noise. When probing a ferrite bead in DC mode, it will read ~0 Ohms (actually tens or hundreds of milliOhms). However, as high frequency noise gets more intense, it will become resistive and dissipate the noise energy in the form of heat. The specs for a ferrite bead are resistance (at a certain frequency) and current capacity.

However, popular wisdom has it that the ferrite bead is more like a “fuse”, blowing when there is excess current. In that sense, you can short the two pads rather than replace it and the phone will work fine afterwards. This works in a pinch but for a professional repair, it should be replaced. In your case, you have put conductive paint and it seems to work but I don’t see this as a long term solution and there is no guarantee that it will work properly depending on the actual resistance of the bridge you created nor it’s current carrying capacity. Too much capacity can allow more current than should safely move downstream to other subsystems.