The forum [PR5], which was the richest and most active part of the site, was put on maintenance mode for 3 weeks. For that time pages were inaccessible and users could only see a maintenance notice.

Before that, as soon as a topic was posted, it was indexed in Google in a matter of minutes and with very high position. Now, it takes even days to get topics indexed and most of them are not.

Is there any way to help the situation?

Yep
Don't ever do it again.

You think there is something I can do now, after this has been done?

No, you'll just have to remove the forum from maintance mode. What happened is now all your forum URLs don't point to their original source, I assume they recieve the same maintance message on every page. This in effect changes the SEO value of each page and will start de-indexing due to duplicate content on multiple web pages.