Welcome, @hughesd
Complicated question!!
Technically you can manually adjust anything that you want to This is how it was all done originally – additions, removals, corrections. You must be extremely careful but it is certainly possible.
You will need to have that all_fasta file itself but it could be empty (no local indexes) or have custom values that link into other custom lines in other custom tables.
But first, do you want to troubleshoot what is going wrong with the Data Manager itself? Was it sourced from the ToolShed? Are you doing other custom adjustments? Are you trying to remove/comment out bad entries that were added?
Or, you can just dive right it! Save a back up before you start!
We have some older administrative docs here with command instructions and general directly structure outlines.
Legacy Advanced Use ONLY May Break Your Database Integrity Galaxy Administration - Galaxy Community Hub
Most of this is deprecated but the Data Resources section has mostly correct information as far as local tables are concerned. If you are also using the CVMFS mount, tread extra carefully. Save back copies to make reverting easier. I wrote and used those guides and might remember how they work if you have a question about the content.
XRef – these are the current definitive safe administrative guides.
Let’s start there! 