If the problem is just of launching two copies at the same time, make the code verify before running that the other copy is not running.
Unfortunately this is not the main problem at the moment. The first thing is that after the most memory consuming part of processing was disabled in one of the copies the bot became more stable. But the main problem is that with the limitation on memory table size just introduced it cannot perform even its very first steps even when runs alone.
The other problem is that once the limit had taken place two years ago I would never go with creating this tool, but I did; and this means I've spent a huge part of my life for nothing and a few other people did the same. One of my collegues who runs the bot and applies its results for ru and uk just participated poland wiki-conference describing the tool and inviting the third language comunity to apply bot's results in their wiki.
mashiah