> Is this because inquisit can only read values from a text file and cannot write/update them?
Yes, that is correct. To keep working with the command line / Windows batch approach, you would instead have to have the batch do the updating work. I.e.
- make sure the variable of interest is logged to the script's data file, using the summary data file is probably easiest.
- after script A is done, have the command line script read in the data file , retrieve the variable of interest, and then update the to-be-included file accordingly.
- then have the command line script invoke script B, which can now read in the updated file per its <inlcude> as usual.
 Inquisit data files are just simple tab-delimited text files, so doing some mild processing and parsing to extract some value via CMD syntax should be possible. https://en.wikibooks.org/wiki/Windows_Programming/Programming_CMD#FOR_Looping
Batch syntax is quite powerful, but has its limitations. On newer Windows systems, you could use the more modern and capable PowerShell instead.