I do it this way:

I've got an installation dir, ( assume z:\install ) and the vpn-files in a subdirectory ( z:\install\vpn ). Furthermore I have three files in the z:\install, namely vpn-setup1.iss

│[InstallShield Silent]
│Version=v6.00.000
│File=Response File
│[File Transfer]
│OverwrittenReadOnly=NoToAll
│[{5624C000-B109-11D4-9DB4-00E0290FCAC5}-DlgOrder]
│Dlg0={5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdWelcome-0
│Count=5
│Dlg1={5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdLicense-0
│Dlg2={5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdAskDestPath-0
│Dlg3={5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdSelectFolder-0
│Dlg4={5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdFinishReboot-0
│[{5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdWelcome-0]
│Result=1
│[{5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdLicense-0]
│Result=1
│[{5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdAskDestPath-0]

vpn-setup2.iss

Result=1
[{5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdSelectFolder-0]
szFolder=Cisco Systems VPN Client
Result=1
[Application]
Name=VPN Client
Version=3.50.000
Company=Cisco Systems
Lang=0009
[{5624C000-B109-11D4-9DB4-00E0290FCAC5}-SdFinishReboot-0]
Result=1
BootOption=0

and vpn.cmd

@echo off
REM Change to the current directory
cd /D %~dp0

REM copy the installation files to the temp directory 
xcopy /IHYQ vpn\* %TEMP%\vpn

REM Create the answer file, independent of the Program fiels directory
type vpn-setup1.iss > %TEMP%\vpn\setup.iss
echo szDir=%PROGRAMFILES%\Cisco Systems\VPN Client >> %TEMP%\vpn\setup.iss
type vpn-setup2.iss >> %TEMP%\vpn\setup.iss

REM Start the silent installation
start "" /wait "%TEMP%"\vpn\setup.exe -s

REM Delete local installation files
rmdir %TEMP%\vpn /S /Q

It's a little fuzzy, but I wanted to have the installation process independent of the location of the location of the programfiles directory.

The xcopy command is only used, because the installation of the client won't run from a network drive.

You could also generate the whole answer file through the batch.

What I did was use the msi version of the Cisco VPN installer. First I made an AIP, then tweaked the msi file using AdminStudio, and finally turned the whole thing into 7-zip based switchless silent installer. This way when you execute the file, it will decompress to the temp directory on the local hard drive and install from there, bypassing the network disconnect problem. The whole thing compresses down to 4.15MB too.