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Our site is an online clinic Management System that is developed with AngularJs.
I put structured data objects in JSON-LD format and just because our site is single page, I put general json-ld (@type: Organization) in layout, and dynamically add breadcrumb (@type: BreadcrumbList) and webpage (@type: WebPage) or article (@type: NewsArticle) data for each page.
Google Structured Data Testing Tool detect all my objects, and after a while They appeared in my Google Search Console.
The problem is, after I replaced the (@type: Organization) json-ld in layout, with another json-ld (@type: WebApplication), google testing tools still show them, but all my other detected Structured Data in search console gone!

You can check my data live here.

Is there any conflicts between structured data objects?
For example: we cannot put any other structured data beside (@type: WebApplication)!

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your WebApplication snippet can't be recognized as those, because it isn't JSON-LD: Your organization snippet begins with: <script type="application/ld+json">

But your WebApplication snippet begins with: <script id="mainJsonLd" type="text/ng-template">

After i changed it to <script type="application/ld+json"> WebApplication is recognized like a charm: enter image description here

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