I haven't tried to duplicate the issue, but I can see that it could happen. After all CodeTools (eg: code completion, parameter help etc) fails to work when code is not compilable either - very annoying.
I can't test your help issue locally, because I reassigned the F1 key in Lazarus IDE to my own help system, using fpGUI's Docview help viewer and the help files being in the INF file format. This is definitely not affected by code that can't compile - after all, if you can't remember the syntax for something, you would like to press F1 to get help on that topic. So having a broken help system at that point would be a double whammy.
You are welcome to try DocView. It is set up via the IDE's External Tools functionality, so no need to install new packages and recompile your IDE.
http://fpgui.sourceforge.net/docview_ide_integration.shtmlPre-compiled binaries of DocView are available on SourceForge. INF help files for Free Pascal's RTL, FCL, Language Reference, as well as fpGUI and LCL API docs are also available from fpGUI's SourceForge page in the Files section.