We increase the BW to our clients at night. To do so we have scripts that disable the ether interface on which PPPoE server is running at a set time and enable it again a minute later. In this minute interval another scheduled script is run which changes profile limits.

This procedure is repeated at the end of the enhanced BW period with the profiles being set to normal again.

Is there a better way of doing this?

As usual with MT, you have more than one way to make thing done (it's like programming in perl :) :
1. First change the limit, anf then remove all PPPoE clients or disable-enable the server (there is no way to change the limit on the fly). This will minimize the "black hole" for the clients
2. Use PCQ on your clients, not the PPPoE limits - you will have to use tree queues, consult the manual on how to do this. AFAIK, then you will be able to change limits on the fly.

2. Use PCQ on your clients, not the PPPoE limits - you will have to use tree queues, consult the manual on how to do this. AFAIK, then you will be able to change limits on the fly.

PCQ ?????

Per Connection Queuing - each user will have the same bandwidth. See the Bandwidth Control manual for more info.