Yes, if a castle is taken, its investments are resetted.
From agit_main.txt:
...
OnAgitBreak:
...
// Refresh castle data, disable Kafra and reset Invest information.
donpcevent strnpcinfo(0)+"::OnRecvCastle";
disablenpc "Kafra Staff#"+strnpcinfo(2);
for( set .@i, 4; .@i <= 9; set .@i, .@i+1 ) {
SetCastleData strnpcinfo(2), .@i, 0;
}
...