Assuming you're running Ekos on the same machine as the files are being stored, I'd guess you're running into the scheduler option "remember job progress"
You could turn that off, though it is useful when jobs are started and suspended and resumed. You could also do what Jasem suggested and move your fits files after the first job is done.
If you want to look into debugging things...
If you run with debug logging for the scheduler, your logs will contain lines like this:
[2022-09-28T19:46:26.073 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/m77/Light/Red/NGC_7320_Light_Red_240_secs" : 3
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - Frame map summary:
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/NGC_7320/Light/Blue/NGC_7320_Light_Blue_240_secs" : 40
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/NGC_7320/Light/Green/NGC_7320_Light_Green_240_secs" : 40
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/NGC_7320/Light/LPR/NGC_7320_Light_LPR_120_secs" : 286
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/NGC_7320/Light/Red/NGC_7320_Light_Red_240_secs" : 40
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/m77/Light/Blue/NGC_7320_Light_Blue_240_secs" : 0
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/m77/Light/Green/NGC_7320_Light_Green_240_secs" : 0
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/m77/Light/LPR/NGC_7320_Light_LPR_120_secs" : 43
[2022-09-28T19:46:26.075 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "/home/pi/mydisk/m77/Light/Red/NGC_7320_Light_Red_240_secs" : 3
[2022-09-28T19:46:26.076 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'NGC 7320' 15x120\" LPR completed its sequence of 0 light frames."
[2022-09-28T19:46:26.076 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'NGC 7320' 8x240\" Red completed its sequence of 0 light frames."
[2022-09-28T19:46:26.076 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'NGC 7320' 8x240\" Green completed its sequence of 0 light frames."
[2022-09-28T19:46:26.076 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'NGC 7320' 8x240\" Blue completed its sequence of 0 light frames."
[2022-09-28T19:46:26.076 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'NGC 7320' 35x120\" LPR completed its sequence of 0 light frames."
[2022-09-28T19:46:26.076 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "Job 'NGC 7320' is configured to loop until Scheduler is stopped manually, has undefined imaging time."
[2022-09-28T19:46:26.077 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'm77' 15x120\" LPR completed its sequence of 0 light frames."
[2022-09-28T19:46:26.077 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'm77' 8x240\" Red completed its sequence of 0 light frames."
[2022-09-28T19:46:26.077 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'm77' 8x240\" Green completed its sequence of 0 light frames."
[2022-09-28T19:46:26.077 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'm77' 8x240\" Blue completed its sequence of 0 light frames."
[2022-09-28T19:46:26.077 PDT INFO ][ org.kde.kstars.ekos.scheduler] - "Job 'm77' 35x120\" LPR completed its sequence of 0 light frames."
[2022-09-28T19:46:26.077 PDT DEBG ][ org.kde.kstars.ekos.scheduler] - "Job 'm77' is configured to loop until Scheduler is stopped manually, has undefined imaging time."(Obviously those lines that says "completed its sequence of 0 light frames" is a buggy log line, I'll look into that).
In the above, you can see how it figures out how many captures are completed, e.g. by notiding there were 40 files that started with
"/home/pi/mydisk/NGC_7320/Light/Blue/NGC_7320_Light_Blue_240_secs"Read More...
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