Reintroducing Noise to a Spliced Signal

Hi everyone! I'm running into an issue and I can't figure it out for the life of me.

Some background: I am trying to analyze some ECG data. I've got a binary matrix in which the 1s represent detected heartbeats. I convolve through this binary matrix with a gaussian filter to find the heart-rate.

However, there's some noise in the data. We would just replace the noise with NaN's in the binary matrix, but that would produce edge effects (since no data is flowing during NaN segments).

So our new plan is to completely cut out the noisy segments, and run the convolution on that truncated binary matrix, and then reintroduce the noise. However, I'm unsure on how to reintroduce the noise to the array, as the indices of the noise change since the signal is now smaller.

Apologies if the explanation is vague. Let me know if i can clarify. However, here is the code (somewhat messy):

pcs=[];
hrpcs=[];
c=1;
for seg=1:floor(sesLen/5)
    pcs(seg,:) = dum(c:c+750);
    hrpcs(seg,:) = fHrt(c:c+750);
    tpcs(seg,:) = rFTim(c:c+750);
    c=c+750;
end
testt = rFTim; %this is the time-values for the time series
testhrt = fHrt; % these are the Y axis values for the ECG data
nandummy = zeros(size(rFTim,2),1);
dum2 = dum; % dum is the original binary matrix with heartbeats as 1
slct_intv = [];
slct_intv_t = [];
fixhrt = fHrt;
fixt = rFTim;
%display a 5 sec piece of data
f = figure;
for seg = 1:size(pcs,1)
    hold on
    l = tpcs(seg,:);
    p = plot(tpcs(seg,:),hrpcs(seg,:));
    pk = plot(l(logical(pcs(seg,:))),zeros(size(l(logical(pcs(seg,:))),2),1),'ro');
    
    %wait for button press, if mouseclick then go to ginput(), if keyboard
    %skip to next 5 sec piece of data
    w = waitforbuttonpress;
    if w == 1
    elseif w==0
        %get cursor coords
        [x1,y1] = ginput(1);
        [x2,y2] = ginput(1);
        %get nearest value
        [m1,i1] = min(abs(rFTim - x1));
        [m2,i2] = min(abs(rFTim - x2));
        %Get next nearest heartbeat
        for i = i2:size(rFTim,2)
            if dum(i) == 1
                lstbeat = i;
                break
            end
        end
        %reset i to lower limit
        i = i1;
        % get last nearest heartbeat
        while i >= 1
            if dum(i) == 1
                frstbeat = i;
                break
            end
            i = i - 1;
        end
        
        % edit dummy data
        nandummy(frstbeat+1:lstbeat) = NaN;
        lstbeat_time = testt(lstbeat);
        frstbeat_time = testt(frstbeat);
        slct_intv = vertcat(slct_intv,[frstbeat lstbeat]);
        slct_intv_t = vertcat(slct_intv_t,[frstbeat_time lstbeat_time]);
        % Remove selected data
        testt(frstbeat+1:end) = testt(frstbeat+1:end) - (lstbeat_time - frstbeat_time);
        testhrt(frstbeat+1:lstbeat) = [];
        testt(frstbeat+1:lstbeat) = [];
        dum2(frstbeat+1:lstbeat) = [];
        
    end
    cla(f);
end