That is a possibility if the seals are worn out. They will be flattened by having the top on but if they are still supple, it shouldn't be a problem. Just make sure the bolts are snugged up when you put it back on. Leave the side bolts loose and tighten the ones around the cab first then work your way from front to back tightening them one at a time keeping even on both sides. Test it afterward with a hose, if it leaks snug up a little more. If you tighten the side bolts first, then it will work against getting it snugged up against the cab.
If the seal are hard, then you probably should think about replacing them. Early FSB had bolts that were easily removed, later ones haave security bolts and require a security ***** driver, (they have a rejection tip inside the head of the bolt).
Good luck,

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PS
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