I use my Mikrotik RB3011UiAS to connect to my fibre ISP here in New Zealand. A few months ago, I noticed that after updating my router, my internet connection did not come back after the reboot. I contacted the ISP who insisted that everything was 100% fine their end and that they could see me attempting to make the connection, but it was unsuccessful for reasons they couldn't explain. They blamed my router. It was only after powering down my ONT on the wall and waiting 10 minutes that the PPPoE connection was successful. Ever since that day, I have been unable to disconnect and reconnect my PPPoE interface without powering down the ONT for 10 minutes. Any hope of remotely updating the router when a new version of RouterOS is released is out the window, since I know that it won't come back online afterwards. It's very frustrating to say the least.

Last night I thought I'd try the Huawei router that came from my ISP when I signed up. As it turns out, the Huawei was able to disconnect and reconnect at will without the need to touch the ONT at all.

I've used Mikrotik routers in various flavours for as long as I can remember now and I have never experienced this problem but there is clearly an issue. I find it very hard to believe that my hardware is faulty since once it is connected, everything runs like a dream and fortunately, the connection stays active for weeks or even months without the need to touch the ONT. However I would love to get to the bottom of this, so if anyone has any ideas, I'd really like to hear them please.

Thanks in advance.

Looks like your PPPoE session got stuck, most likely ISP's equipment didn't like how it was closed by mikrotik.
Also a limit of one session per user at a time is set up, as is pretty common for providers.

BUT - usually PPPoE servers have pretty short keepalive timeout - a couple of minutes at most, after which dead sessions are terminated.
Also without any action on the user's side. And I don't know why support guys couldn't force terminate your session.