We're aware of an issue whereby certain ship parts are missing when you log in. This most notably applies to decks and panels but can impact other objects too.
As far as we know, the parts themselves are not damaged or destroyed (they are still visible in our systems) but they are not loading in: therefore they will be invisible / not have collision on the client but will on the server. If you move your ship somewhere else they should come back after a relog.
Note: if your ship is in this state and you place parts over the missing ones, it is likely they will load in at some point at cause weird things and potential damage to your ship. We suggest moving to a different area first to confirm this is the case before rebuilding.
We're working on a fix for this that will hopefully be incorporated into the next hotfix/update to 29. ETA TBC.