I am recording a 30 second 1000Hz Sine wave, saving it to a list, splitting the list into 5 second sublists and I would like to apply a notch filter to each sublist to check when the signal drops out for a few samples (I'm filtering out the 1000Hz frequencies). I am using python along with scipy for signal processing. I had some success using this method when I recorded the signal and applied a filter to the entire signal at once, but whenever I try to apply a filter consecutively to 5 second chunks of the signal, I seem to detect glitches that aren't there.
Here is the code for my filter.       

       f0 = 1000.0  # Frequency to be removed from signal (Hz)
        Q = 30.0  # Quality factor
        w0 = f0/(fs/2.0)  # Normalized Frequency
        # Design notch filter
        b, a = signal.iirnotch(w0, Q)
        sos = signal.tf2sos(b,a)
        zi = signal.sosfilt_zi(sos)*lists[0][0]
        for list in lists: #each list is 5 seconds long
            Time=np.linspace(0, len(list)/fs, num=len(list))
            plot_graph(Time,list,fs)
            y_sos, zi = signal.sosfilt(sos, list, zi=zi*list[0])
            plot_graph(Time,y_sos,fs)

The graph below shows the first filtered 5 second chunk.
[![enter image description here][1]][1]


The large peak just after one second is a genuine dropout but the 3 smaller peaks should not occur at all.

The graph below shows the next filtered 5 second chunk
[![enter image description here][2]][2]

There are no glitches at all in this section, yet the small peaks still occur. I would also ideally like to get rid of the peak that begins at 0 and 5 seconds of each chunk.
Can anyone tell me what is wrong with my filter/method?


  [1]: https://i.sstatic.net/sj1QK.png
  [2]: https://i.sstatic.net/GbxHg.png