This can happen when Geneious is updated and reverts to the default memory setting, which is too small to handle large files in your Geneious 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.
On Windows it is in the file Geneious.default.64bit.vmoptions and/or Geneious.in.use.vmoptions, which is in the Geneious folder in Program Files.