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I am storing all my autographs in acid free/archival safe protective sleeves but for some reason it lifts off the print of SILVER sharpied autographs. Does anybody know what i should do?

Silver sharpies and similar paint-style pens are notoriously difficult to store as they tend to wipe off. You need to secure the signatures as much as you can, by spraying them with a fixative spray or if you cant find one, hairspray will do the job. When it's dry, store them as normal and they'll be easier to handle.

is there any other item I can use? Like a special folder? I am uncomfortable spraying chemicals onto my autographs

^ no, anything touching it will risk smudging the autograph, just like the archival sheets do. Fixative spray is made for (as the name suggests) fixing substances on paper, usually charcoal or pencil drawings. Hairspray will do the job too. You can even get archival quality fixing sprays which wont damage the autograph, if you're worried.