how to correctly upload a WAR file to the file system in Liferay 7.3.5

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Using Liferay 7.3.5, i am consistently running into issues regarding theme deploy. I am trying to upload a theme to my server using the instructions given in the following guide:

https://learn.liferay.com/dxp/latest/en/system-administration/installing-and-managing-apps/installing-apps.html

When i try uploading apps via the file system and into the deploy folder, the file appears to vanish and nothing happens. I have since been uploading it directly to the WAR folder, but i am now running into some issues when a theme is deployed that way.

I expect the theme to be uploaded and working properly, the CSS to be applied to the page(s) and the liferay menu to be intact.

Uploading the theme appears to go well and the theme shows inside the list you can choose from. Inside the list however, the theme doesn’t display a thumbnail. Problems started once i uploaded multiple themes to the same liferay server. On the site pages, the CSS is not properly applied and looks broken as if there isn’t any theme applied. The edit page button on the top right is invisible, as are the rest of the menu items.

Publishing the site or reselecting the theme do not resolve the issues, nor did a redeploy of the theme.

Does anybody know how to correctly upload a WAR file to the file system in Liferay 7.3.5, or am i overlooking something else?

UPDATE 22/09/2022

so i have narrowed down the issue a bit. When i first upload a theme to my war folder is works fine. However when deploying a another theme, the first one breaks. I doesn't really matter which of the theme's i use as it seems to do it for all of them, I created a github with two simple theme war files. If you want to reproduce the issue. https://github.com/Lincolnmyth/theme

All you have to do is follow the normal steps and upload the theme. Turn the server on, and check if it works. Then turn it back off again to add another one. You'll then start seeing issues in the first theme. Such as liferay buttons changing the same colour as the background and the css from the theme not working. So for example, the januari theme should change the navbar and add a picture about it. If you upload the other theme however this doesn't work anymore.

I hope this works as a reproducible example

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