The journal editor accepted my paper and told me to ask his assistant about the next steps in the publication process. Four months ago I corrected some minor points and sent an updated manuscript to the assistant. Since then the editor's assistant remained silent. About two weeks ago I asked him about the status of the manuscript and next steps, but he hasn't replied yet. What should I do? Could the editor reject my manuscript after acceptance?
You should write to the editor and tell him what you have told us. Really your concrete problem is that your correspondence has not been returned so you don't know what's going on. Maybe everything is proceeding as it should, maybe it isn't, but you need a reply.
Could editor reject my manuscript after acceptance?
Why do you even ask? Are you worried that the editor thought, "No, hang on, I don't want to publish this paper after all. Let's not publish it, never contact the author again, and hope for the best"?!? That's just totally loopy, unprofessional behavior. In this big, bad world of ours, anything could happen, but the chance of this happening to you -- provided only that you are dealing with a partway reputable, professional journal (essentially: not a journal that you learned about via a spammy, semi-literate email) -- is negligibly small.
Just get back in contact with the editor ASAP and take it from there. Be polite, but be persistent. Give the editor a week or two to reply. I honestly expect that he will. If not, write to the editor-in-chief / managing editor / some other members of the editorial board. You'll hear back from someone. Again, don't assume that something has gone terribly wrong, and certainly don't worry that your polite, professional behavior will jeopardize the future of your paper.
You should write to the editor explaining that you have not received any further communication about the status of your manuscript for the last four months and that the assistant has not replied to your e-mail. I'm sure you will receive a reply from the editor. If you do not receive a reply from the editor within a couple of weeks, try to get hold of his number and call him. If that doesn't work, write to the editor-in-chief or managing editor of the journal.
Regarding your second question, once a manuscript has been accepted, the decision cannot be reversed, unless a major ethical breach, such as duplicate publication, salami slicing, or undisclosed conflict of interest, has been detected. However, if your manuscript free from these problems, you need not worry: it will not be rejected.