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I am asking myself what is the best when storing a 3.5 disk drive for a long time but still planning to use it in the future, what is the best: Store it with a disk inserted, or leave it empts ?

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Leave it empty. In floppy drives, the read/write head touches the disk’s surface, so leaving a disk inserted for long periods of time can cause problems — the head will tend to stick to the surface, pulling it off when the drive is next powered up.

Some drives shipped with a cardboard insert which was intended for use in shipping and long-term storage, but that was more common with 5.25” and older drives. Some drives also have shipping screws to lock everything in place, but I wouldn’t expect that on a 3.5” drive.

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    Some 3.5" drives shipped with a plastic insert for shipping but I don't think they are needed for storage -- I believe there are intended to limit head movement during shipping while also preventing the heads from touching (or damaging) each other – Ken Gober Apr 22 '18 at 15:09
  • @KenGober In case you still have them, it would probably not hurt using them for long-term storage. – tofro Apr 22 '18 at 17:43
  • I agree, it wouldn't hurt to use them if you have them. But if you don't have them I don't think you need to go out of your way to get them if all you care about is storage. They might be worth the effort to acquire if you're planning to ship a drive though. – Ken Gober Apr 23 '18 at 1:51
  • The cardboard or plastic insert was only used to secure the head sled (from getting pushed around by inertia and potentially slamming into the limits). All I've seen have a hole for the heads so they don't touch the insert. – Zac67 Apr 24 '18 at 11:51
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in addition to Stephen Kitt answer I need to add:

Do not store your FDD closed not even with the dummy carton/plastic disc!!!

  • For 5.25" floppy insert the carton dummy disc but leave the FDD open.
  • For 3.5" do not even insert disc !!!

The carton or plastic sheets (dummy discs) are just for transport to prevent head crushing during unexpected G-force. But in case of long-therm storage You might damage your drive. However the head should be fine on the carton/plastic but the Head load mechanism might not due to two reasons:

  1. compressed head load springs lose strength over time

    The spring will change the shape when stored in closed/inserted position of the head load mechanism. (the same applies for any springs for example there are specific ways how to store bows for the same reasons)

  2. material damage

    Another downfall of the inserted/close storage is that on some FDD drives some parts of the head load mechanism are from plastic which tend to change its properties if long therm force is applied. I have one drive damaged like this only after few years of storage (was necessary to reinforce one plastic bridge with metalic plate to repair the damage and make the head load working again. I got it as spare parts as it was inoperable and after repairing it I got fully functional D40 FDD+FDC which was too expensive at that time for me and could move forward from tapes :) and it is still working till today)

Both problems are affecting the Head load force and position causing read/write errors making the drive inoperable (only due to mechanical reasons).

So It is better to leave the heads in the open/non-inserted position and the best option is to use the fixating screws in open position if present (which is improbable).

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