Can you provide an example of a past technology that was unimagined by mainstream physicists and that was sucessfully implemented in secret and kept secret for decades?

I can't think of anything.

Fission bombs were widely believed to be physically possible, were developed in secret but used publicly within several years.

I do not beleive the military has some secret antigravity, inertia modifying technology or warp drive of whatever.

These things always start with basic physics. There is no known basic physics to support such things. Therefore it is extremely unlikely that the military simply developed them from theory to implementation in secret.