Your tools are gone from the Navigator after closing and reopening MT5.
They were saved to the wrong data folder, or a different installation is being opened.
Each MetaTrader installation keeps its own separate data folder, and the Navigator only ever shows the contents of the folder belonging to the copy you have open. If you have installed the platform more than once, which happens easily when you have accounts with two brokers, files placed in one installation's folder are genuinely invisible to the other. Nothing has been deleted; you are looking at a different filing cabinet.
The other cause is placing files into the installation directory rather than the data folder. On Windows those two locations are separate by design, so that the terminal can write without administrator rights, and a file that lands in the program directory is never scanned. It may appear to work in the moment if the terminal was already running with the file loaded, only to be absent after a restart.
Open the data folder from inside the running terminal, so you are certain you are looking at the right one, and confirm your files are in the indicators or experts subfolder there. Refresh the Navigator and check the tools appear. Then restart the terminal and check again, since surviving a restart is the actual test.
Only ever install files by opening the data folder from within the terminal you want to use them in, never by browsing to a path from memory. If you must run two installations, pin them separately and label them clearly so you know which is open. Keep a copy of your indicator files somewhere outside the platform, as an uninstall or clean reinstall can take the data folder with it.
Market Structure Pro gives one clear TRADE or NO-TRADE verdict on any MT5 chart, with confidence, grade and a plain-English reason. Free 7-day trial, no card.
Start free trial