How can I Merge Workbooks?

Merging workbooks is not a simple operation.
Errors are possible when appending rows to the edges and vertices worksheets.
One approach is to turn off an option in NodeXL>Data>Import>Import Options that clears the workbook before importing new data.

You may also be interested in this: https://www.connectedaction.net/product/connected-action-graph-server-importer/ which enables NodeXL to accumulate data from the Twitter API over time.
If you do decide to paste multiple workbooks together please consider the following issues and steps.
  • NodeXL uses “Named Ranges” for all of the tables and worksheets.  Pasting new data in the first blank row may not extend the named range for edges, or it may break the existing named range.
SOLUTION: Paste INSERT the new rows in the edges the worksheet, starting in a row above the last row.
  • Pasting data from multiple Edges worksheets can create duplicate Edges
SOLUTION: Be sure to remove duplicate rows before analyzing the new aggregate workbook.
  • Pasting data from multiple Vertices worksheets can create duplicate vertices – which NodeXL does not like : -(
SOLUTION: Be sure to remove duplicate rows before analyzing the new aggregate workbook.
You will then need to recalculate all metrics (or just re-run NodeXL>Graph>Automate>Run) to analyze all the new data in your network.
Also note: NodeXL networks have size limits based on the computer resources available.  Critically, RAM is a requirement for large networks.  If you are merging many networks you may quickly create a VERY LARGE network which will create issues of its own.