I have a rather large reactor that happens to span a corner of 4 chunks. The reactor can hold about 1500 yellorium at maximum capacity. If I warp to a different realm (nether, moon, etc.), and am at that location long enough for the chunks containing the reactor to completely unload, then warp back, occasionally the contents (yellorium, blutonium, cyanium) are missing after the reactor reassembles from the load. This is especially true if the chunks take some time to load (more than 20 seconds) after using the /home command. I cannot get it to reliably recreate itself, but it may be that I don't have enough information about the conditions when the issue occurs.

A second way to destroy the reactor's contents is using the manual fuel eject button on any input or output port. In my instance, the Applied Energistics ME system connected to those ports did not sweep the contents out when the eject fuel button was pressed. Fuel was ejected to all ports (input or output) instead of only the port with the active GUI. Lastly, if the eject fuel was pressed a subsequent time before the stacks of fuel were removed from ALL ports, the reactor assumes that all ports were empty anyway and reduces the fuel in the reactor accordingly, even if no new ingots were made available. These may be related issues.

I'm unable to reproduce the first problem.

The second problem will be fixed for 0.3.3A, thanks for the report.

In the future, please report different bugs in separate issues.

I've not been able to reproduce the "accidental fuel destruction" by only pressing the eject fuel/waste buttons. However, that behavior can be intentionally triggered by holding down the Shift key - this instructs the port to "dump excess", which means it will remove any excess fuel/waste that could not be ejected into ports.