If you want to add an internal link to your RMD, that is reference the appendix from the summary section, ex:
summary
link here to heading 2 of appendix section
appendix
Heading 2 of Appendix
you would add the following (note this is case-sensitive, everything is now lower-case and spaces are exchanged with hyphens):
# summary
**[name of link](#heading-2-of-appendix)**
```{r}
```
# appendix
```{r}
```
## Heading 2 of Appendix
Also, note that in the reference to the heading-2-of-appendix, there is only one #, regardless of the type of heading the section-to-be-referenced is in.