Currently it is possible to stupidly lose mempool data by calling the rpc "savemempool" before the previous stored mempool has been read and processed to the memory mempool.

I haven't looked at the code yet, but at minimum one ugly solution would be to have a global g_is_mempool_read_finished (or something of the short) that starts false and gets sets to true once the reading is reading processing of mempool.dat is successfully finished. The rpc savemempool checks this global on the start and returns a an error while it remains false.

assert(!blocksConnected.back().pindex);
        assert(blocksConnected.back().conflictedTxs->empty());
        blocksConnected.pop_back();
        return blocksConnected;
    }
    void NotifyEntryRemoved(CTransactionRef txRemoved, MemPoolRemovalReason reason) {
        assert(!blocksConnected.back().pindex);
        if (reason == MemPoolRemovalReason::CONFLICT) {
            blocksConnected.back().conflictedTxs->emplace_back(std::move(txRemoved));
        }
    }
};
/**
 * Connect a new block to chainActive. pblock is either nullptr or a pointer to a CBlock
 * corresponding to pindexNew, to bypass loading it again from disk.
 *
 * The block is added to connectTrace if connection succeeds.
 */
bool CChainState::ConnectTip(CValidationState& state, const CChainParams& chainparams, CBlockIndex* pindexNew, const std::shared_ptr<const CBlock>& pblock, ConnectTrace& connectTrace, DisconnectedBlockTransactions &disconnectpool)