This can happen when Geneious is updated and reverts to the default memory setting, which is too small to handle large files in the database. To fix this you need to reset the memory allocation for Geneious by opening the vmoptions file for Geneious and increasing the –Xmx setting to the amount of MB you want to allocate to the software.
On a mac this is in the info.plist file which you can find in the Geneious.app folder by right clicking on it and selecting Show Package Contents and then going into Contents.
Note that you will find two instances of -Xmx in the info.plist file.
For Macs using a 32-bit operating system, edit VMOptions.i386-Xmx1000M
For Macs using a 64-bit operating system, edit VMOptions.x86_64-Xmx1000M
On Windows it is in the file Geneious.default.64bit.vmoptions and/or Geneious.current.vmoptions, which is in the Geneious folder in Program Files.