Everything you ask can be done by development.
1st Question - Is there a way to create a dynamic file or customized report (that can be converted to excel)?...
Is this possible?
There was an addon for this, but I think it's not tested in a recent Alfresco versions but it could be a good starting point for your idea.
2nd Question- Delete, I need to mark a file like deleted but not really delete it. The file should still be on site possession be reported on the report mentioned on the previous question. Something that shows visually that the file is different.
Yes. You can implement your own status (like "mark as archive", e.g.), develop the behaviour and get it working. But it's not simple.
3rd Question - Interact with properties metadata without the need to edit properties. File type is defined by folder ou by file upload form.
Unfortunately, there is way to do this OOTB. However, you can implement custom bulk metadata update functionality.
1- Implement a java backed webscript to generate the list of nodes refs and their current metadata in the excel sheet. This webscipt will read the folder node and find all files (even from within nested folders), and get the properties from each file/content nodes and write them into the sheet. You would get the row wise metadata/properties for each node. You must include the nodeRef in the sheet which will be used for updates later. You can write this sheet into logged in user's "MyFiles" directory, user can download the sheet from there and later upload a new version of it with updated metadata.
2- Implement an action on folders (folder-browse/folder-details) to allow generating the sheet which will be used for bulk metadata update
3- Implement an action on the Sheet which was written under "MyFiles", so user can then click to update the metadata in bulk after uploading the sheet with updated metadata as a new version of existing sheet.
4- Implement another java backed webscript which will update the metadata in bulk based on input sheet (generated as part of 1st step). It will read the existing node metadata/properties based on nodeRefs by processing row by row and then apply newly updated metadata by parsing the row for that particular nodeRef.
Note-Consider restricting updates to read only properties such as "created date,modified date,creator,modifier,node-uuid" etc. or any others based on your current business needs.
1- Implement an action in multi select action menu to select multiple files at once.
2- Implement a form that loads common and allowed (not restricted) metadata properties for updates
3- Use the ootb form processor to save the updates.
Take a reference from this post; http://alfresco.blog.redpill-linpro.com/2014/06/25/bulk-edit-of-metadata/