If the boundary condition type (e.g., inflow velocity profile or RCR conditions) does not change (even if the values do), AND the mesh does not change, it is absolutely possible to automate the process.
You would have to manually generate bct.dat files and/or rcrt.dat for each simulation, then have them in the corresponding folder with the geombc.dat.1 and restart.0.1 and solver.inp files.
The structure of the rcrt.dat is very simple, so you should know how to modify that file for each simulation.
The format of the file is as follows:
np nl
x1 y1 z1 nl
vx1 vy1 vz1 t1
. . . .
. . . .
. . . .
vxnl vynl vznl tnl
.
.
.
xnp ynp znp nl
vx1 vy1 vz1 t1
. . . .
. . . .
. . . .
vxnl vynl vznl tnl
The file defines the spatial and temporal definition of the inflow boundary condition. np is the total number of nodes on the face “inflow”.
The temporal definition is given by nl input lines of the values at a certain position for nl time points, t1 to tnl.
I hope this helps.