I have encountered this issue using my N900 with a bicycle hub dynamo/eWerk charger system, in the end I put a switch that I flip to disconnect/reconnect the charging and short on the data pins ever few minutes. Crude as can be but works.
The N900 will restrict itself the the previous amps once it detects any voltage drop, sometimes it will drop to zero and it will not reset until disconnected. I dug around a few years ago and tried add a reset script to the BME every 5 min to renegotiate the charging amps but it didn't work and killed charging/USB completely until I reverted.
I don't have the skills to make it work but I think it would be easy for someone in the know, much as bypassing the shorted pins in code would probably be doable. OTOH it might be a hardware limitation in the BME, I don't know.
This app could be useful to many, consider putting it on the unstable repos.