Source for header image: The Creative Spark https://www.youtube.com/watch?v=vrvawtrRxsw
Activate Markdown
If you go to the top menu bar and select Zettelkasten - Preferences and then the General tab you will find a tickbox called ‘Activate Markdown’. If you tick the box you will find strange things happening to your Notes, your lists look messed up, headings disappear, photos vanish, and some Notes may fail to display. Do not panic, as unticking the box and everything will return to normal.
Location of the Activate Markdown tickbox
Clearly the intention of the programme designer was to allow users to switch from the proprietary markup used in Zkn3 to Markdown markup. To the user, this may be just a personal preference but it could be an advantage when migrating to another zettelkasten type programme and make it easier and require less post-processing. Or your style of zettelkasten may be fairly minimalist and text based and so suit a Markdown style.
The problem is that Zkn3 simply does not implement Markdown syntax in full and while some Markdown code works in the programme other parts do not work. So text in BOLD in Zkn3 are marked by [f] text [\f] and the Markdown equivalent **text** works equally well. But HIGHLIGHTED text in Zkn3 is marked by [h #ff00ff]text highlighted[/h] however the Markdown equivalent ==text highlighted== does not work. Probably the largest issue is tables which do not display correctly when written in Markdown style. Moreover some Notes with tables refused to display when the Markdown tick box was selected.
On balance, my recommendation is to ignore the Markdown option and leave it unticked. The reason for this is that Zkn3 simply does not work smoothly when it is selected and most of the pre-processing that you want to do to prepare your file for migration to Markdown can be done quite easily from within Zkn3 using the Find/Replace option. Also the Zkn3 version gives you a much richer text experience using its proprietary script.
So here are my recommendations as to what changes can be made from within Zkn3, before you download your Markdown file.
Do not need converting as work in both Zkn3 and Markdown
Hyperlinks
Basic text
Conversion of Zkn3 before migration
Perhaps the easiest way is to save your Zkn3 file as a new file and work on that to convert to Markdown and preserve your original file in Zkn3 format.
Text formatting,
Bold
Find [f] and replace with **
and Find [/f] and replace with **
Italic
Find [k} and replace with _ (underscore)
And find[/k] and replace with _ (underscore)
Strikethrough
Find [d] and replace with ~~
Find [/d] and replace with ~~
Highlighted
Find [h #ff00ff] and replace with == (change code to whatever colour it is you use as highlighter.
Find [/h] and replace with ==
subscript
Find [sub] and replace with ~
Find [/sub] and replace with ~
Superscript
Find [sup] and replace with ~
Find [/sup] and replace with ~
Headings
Find [h1] and replace with # ([h2] with ##, and so on)
Find [/h1] and replace with blank space to delete it ([/h2] etc as well)
Underlining is not supported in Markdown
So simply Find [u] amd [/u] and replace them with a blank space to remove them.
Lists
Find [l] and replace with blank space to delete it
Replace [*] with - or *
Replace [/l] with blank space to delete it
Images
Replace [img] with 
Keywords
Replace 'spaces' with hyphens -
Replace hidden symbol ^ with #
This converts the Keywords into Markdown Tags #markdown-tags
Conversion of Zkn3 markdown files in Notepad++
Cross references
Note sequences
Manual Cross references
Problems
Tables really should be manually changed. You can use the Find command to search for them using [table] as a search term
Zkn3 format is shown as below:
[table]
[tc]table heading[/tc]
Heading1^Heading 2^Total
Line 1|xxx|xxx
[/table]
And convert into Markdown table format as shown here:
| Heading 1 | Heading 2 | Total |
|---------—--|-——--------|-—----|
| line 1 | xxx | xxx |