I can't tell you how Brainstorm would behave with your manually modified FIF files, it depends how the information is saved in them.
function [sFile, ChannelMat] = in_fopen_fif(DataFile, ImportOptions, nLink)
% IN_FOPEN_FIF: Open a FIF file, and get all the data and channel information.
%
% USAGE: [sFile, ChannelMat] = in_fopen_fif(DataFile, ImportOptions, nLink=1)
% [sFile, ChannelMat] = in_fopen_fif(DataFile)
%
% INPUT:
% - ImportOptions : Structure that describes how to import the recordings. Fields directly used:
% => Fields used: ChannelAlign, ChannelReplace, EventsMode, DisplayMessages
% - nLink : Index in the chain of linked files
% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%
% Copyright (c) University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
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function [ChannelMat, Device] = in_channel_fif( sFile, ImportOptions )
% IN_CHANNEL_FIF: Read a FIF file, and return a brainstorm Channel structure.
%
% USAGE: [ChannelMat, Device] = in_channel_fif( sFile, ImportOptions )
% [ChannelMat, Device] = in_channel_fif( sFile )
%
% INPUT:
% - ImportOptions : Structure that describes how to import the recordings.
% => Fields used: ChannelAlign, DisplayMessages
% @=============================================================================
% This function is part of the Brainstorm software:
% https://neuroimage.usc.edu/brainstorm
%
% Copyright (c) University of Southern California & McGill University
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPLv3
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
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